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Sample records for alternative phylogenetic hypotheses

  1. Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

    PubMed Central

    2009-01-01

    The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies. PMID:21637664

  2. How reliable are human phylogenetic hypotheses?

    PubMed Central

    Collard, Mark; Wood, Bernard

    2000-01-01

    Cladistic analysis of cranial and dental evidence has been widely used to generate phylogenetic hypotheses about humans and their fossil relatives. However, the reliability of these hypotheses has never been subjected to external validation. To rectify this, we applied identical methods to equivalent evidence from two groups of extant higher primates for whom reliable molecular phylogenies are available, the hominoids and papionins. We found that the phylogenetic hypotheses based on the craniodental data were incompatible with the molecular phylogenies for the groups. Given the robustness of the molecular phylogenies, these results indicate that little confidence can be placed in phylogenies generated solely from higher primate craniodental evidence. The corollary of this is that existing phylogenetic hypotheses about human evolution are unlikely to be reliable. Accordingly, new approaches are required to address the problem of hominin phylogeny. PMID:10781112

  3. Testing multiple hypotheses with skewed alternatives.

    PubMed

    Bansal, Naveen K; Hamedani, Gholamhossein G; Maadooliat, Mehdi

    2016-06-01

    In many practical cases of multiple hypothesis problems, it can be expected that the alternatives are not symmetrically distributed. If it is known a priori that the distributions of the alternatives are skewed, we show that this information yields high power procedures as compared to the procedures based on symmetric alternatives when testing multiple hypotheses. We propose a Bayesian decision theoretic rule for multiple directional hypothesis testing, when the alternatives are distributed as skewed, under a constraint on a mixed directional false discovery rate. We compare the proposed rule with a frequentist's rule of Benjamini and Yekutieli (2005) using simulations. We apply our method to a well-studied HIV dataset. PMID:26536168

  4. OPEC behavior: a test of alternative hypotheses

    SciTech Connect

    Griffin, J.M.

    1985-12-01

    Since interpretations of past and future oil price patterns depends on the model chosen, the author tests and compares alternative theories of OPEC as a first step in validating the choice on any one model. The results show that among OPEC countries, the partial market-sharing cartel model is the only model not rejected by at least some of the 11 members and gives the best explanation of production. In comparison with 11 non-OPEC countries, the competitive model could not be rejected for 10 of the 11 non-OPEC producers. This raises the question of why, if OPEC is a cartel, Friedman's predictions have not come true, and introduces new questions for future research. 19 references, 3 tables.

  5. An algorithm for constructing and searching spaces of alternative hypotheses.

    PubMed

    Griffin, Christopher; Testa, Kelly; Racunas, Stephen

    2011-06-01

    In this paper, we develop techniques for automated hypothesis-space exploration over data sets that may contain contradictions. To do so, we make use of the equivalence between two formulations: those of first-order predicate logic with prefix modal quantifiers under the finite-model hypothesis and those of mixed-integer linear programming (MILP) problems. Unlike other approaches, we do not assume that all logical assertions are true without doubt. Instead, we look for alternative hypotheses about the validity of the claims by identifying alternative optimal solutions to a corresponding MILP. We use a collection of slack variables in the derived linear constraints to indicate the presence of contradictory data or assumptions. The objective is to minimize contradictions between data and assertions represented by the presence of nonzero slack in the set of linear constraints. In this paper, we present the following: 1) a correspondence between first-order predicate logic with modal quantifier prefixes under the finite-model hypothesis and MILP problems and 2) an implicit enumeration algorithm for exploring the contradiction hypothesis space. PMID:21147596

  6. An Algorithm for Constructing and Searching Spaces of Alternative Hypotheses

    SciTech Connect

    Testa, Kelly M; Griffin, Christopher H

    2010-01-01

    In this paper we develop techniques for automated hypothesis generation over data sets that maycontain contradictions. To do so, we make use of the equivalence between two formulations: those offirst order predicate logic with prefix modal quantifiers under the finite model hypothesis and those ofMixed Integer Linear Programming (MILP) problems. The equivalence between integer programming and logical satisfiability has been known since Karp'sseminal work in NP-completeness. Other authors have made use of this equivalence to explore efficientmethods of solving the satisfiability problem in the propositional calculus for specific problem types.The work presented here differentiates itself from previous work in that we do not assume that alllogical assertions are true without doubt. Instead we look for alternative hypotheses about the validityof the claims by identifying alternative optimal solutions to a corresponding MILP. We use a collectionof slack variables in the derived linear constraints to indicate the presence of contradictory data orassumptions. The objective is to minimize contradictions between data and assertions represented bythe presence of non-zero slack in the set of linear constraints.

  7. An Algorithm for Constructing and Searching Spaces of Alternative Hypotheses

    SciTech Connect

    Testa, Kelly M; Griffin, Christopher H

    2011-01-01

    In this paper, we develop techniques for automated hypothesis-space exploration over data sets that may contain contradictions. To do so, we make use of the equivalence between two formulations: those of first-order predicate logic with prefix modal quantifiers under the finite-model hypothesis and those of mixed-integer linear programming (MILP) problems. Unlike other approaches, we do not assume that all logical assertions are true without doubt. Instead, we look for alternative hypotheses about the validity of the claims by identifying alternative optimal solutions to a corresponding MILP. We use a collection of slack variables in the derived linear constraints to indicate the presence of contradictory data or assumptions. The objective is to minimize contradictions between data and assertions represented by the presence of nonzero slack in the set of linear constraints. In this paper, we present the following: 1) a correspondence between first-order predicate logic with modal quantifier prefixes under the finite-model hypothesis and MILP problems and 2) an implicit enumeration algorithm for exploring the contradiction hypothesis space.

  8. Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures.

    PubMed

    Aguilar, Catalina; Sánchez, Juan Armando

    2007-06-01

    Gorgoniid octocorals taxonomy (Cnidaria; Octocorallia; Gorgoniidae) includes diagnostic characters not well defined at the generic level, and based on the family diagnosis some species could be classified in either Gorgoniidae or Plexauridae. In this study, we used sequences from the Internal Transcribed Spacer 2 (ITS2) and their predicted RNA secondary structure to both correct the alignment and reconstruct phylogenies using molecular morphometrics for 24 octocorals mostly from the Atlantic. ITS2 exhibited the six-helicoidal ring-model structure found in eukaryotes, and provided 38 parsimony-informative characters. The proposed phylogenies, though differing between sequence- and structure-base results, provided consistent support for several clades. Genera considered part of the polyphyletic genus Leptogorgia, such as Filigorgia, were distantly related to the former in all phylogenetic hypotheses. Main differences among the hypotheses consisted in the placement of Muriceopsis (previously considered from the Plexauridae family) and Filigorgia. Excluding Muriceopsis and an undescribed octocoral from Tobago, Plexaurella and Pterogorgia grouped together as a sister branch of Pinnigorgia spp. but long-branch attraction was evident for the grouping of Plexaurella nutans (another plexaurid) and Pterogorgia citrina. Unexpected results were the divergence between Caribbean genera, Gorgonia and Pseudopterogorgia, which were placed basal respect to Pacifigorgia and Leptogorgia (=Lophogorgia). ITS2 provided support to corroborate observations based on sclerite morphology: species with "capstan sclerites" (e.g., Pacifigorgia and Leptogorgia) were characterized by a long helix IV with one internal loop and a helix V with four internal loops; "scaphoid sclerites" had a predominantly long helix V if compared to helix IV; "asymmetric spiny sclerites" (Muriceopsis, Pinnigorgia and the undescribed octocoral) exhibited one or two lateral bulges in the V helix. Remarkably, Muriceopsis

  9. Evolution of microgastropods (Ellobioidea, Carychiidae): integrating taxonomic, phylogenetic and evolutionary hypotheses

    PubMed Central

    2013-01-01

    Background Current biodiversity patterns are considered largely the result of past climatic and tectonic changes. In an integrative approach, we combine taxonomic and phylogenetic hypotheses to analyze temporal and geographic diversification of epigean (Carychium) and subterranean (Zospeum) evolutionary lineages in Carychiidae (Eupulmonata, Ellobioidea). We explicitly test three hypotheses: 1) morphospecies encompass unrecognized evolutionary lineages, 2) limited dispersal results in a close genetic relationship of geographical proximally distributed taxa and 3) major climatic and tectonic events had an impact on lineage diversification within Carychiidae. Results Initial morphospecies assignments were investigated by different molecular delimitation approaches (threshold, ABGD, GMYC and SP). Despite a conservative delimitation strategy, carychiid morphospecies comprise a great number of unrecognized evolutionary lineages. We attribute this phenomenon to historic underestimation of morphological stasis and phenotypic variability amongst lineages. The first molecular phylogenetic hypothesis for the Carychiidae (based on COI, 16S and H3) reveals Carychium and Zospeum to be reciprocally monophyletic. Geographical proximally distributed lineages are often closely related. The temporal diversification of Carychiidae is best described by a constant rate model of diversification. The evolution of Carychiidae is characterized by relatively few (long distance) colonization events. We find support for an Asian origin of Carychium. Zospeum may have arrived in Europe before extant members of Carychium. Distantly related Carychium clades inhabit a wide spectrum of the available bioclimatic niche and demonstrate considerable niche overlap. Conclusions Carychiid taxonomy is in dire need of revision. An inferred wide distribution and variable phenotype suggest underestimated diversity in Zospeum. Several Carychium morphospecies are results of past taxonomic lumping. By collecting

  10. Evaluating alternative stem cell hypotheses for adult corneal epithelial maintenance

    PubMed Central

    West, John D; Dorà, Natalie J; Collinson, J Martin

    2015-01-01

    In this review we evaluate evidence for three different hypotheses that explain how the corneal epithelium is maintained. The limbal epithelial stem cell (LESC) hypothesis is most widely accepted. This proposes that stem cells in the basal layer of the limbal epithelium, at the periphery of the cornea, maintain themselves and also produce transient (or transit) amplifying cells (TACs). TACs then move centripetally to the centre of the cornea in the basal layer of the corneal epithelium and also replenish cells in the overlying suprabasal layers. The LESCs maintain the corneal epithelium during normal homeostasis and become more active to repair significant wounds. Second, the corneal epithelial stem cell (CESC) hypothesis postulates that, during normal homeostasis, stem cells distributed throughout the basal corneal epithelium, maintain the tissue. According to this hypothesis, LESCs are present in the limbus but are only active during wound healing. We also consider a third possibility, that the corneal epithelium is maintained during normal homeostasis by proliferation of basal corneal epithelial cells without any input from stem cells. After reviewing the published evidence, we conclude that the LESC and CESC hypotheses are consistent with more of the evidence than the third hypothesis, so we do not consider this further. The LESC and CESC hypotheses each have difficulty accounting for one main type of evidence so we evaluate the two key lines of evidence that discriminate between them. Finally, we discuss how lineage-tracing experiments have begun to resolve the debate in favour of the LESC hypothesis. Nevertheless, it also seems likely that some basal corneal epithelial cells can act as long-term progenitors if limbal stem cell function is compromised. Thus, this aspect of the CESC hypothesis may have a lasting impact on our understanding of corneal epithelial maintenance, even if it is eventually shown that stem cells are restricted to the limbus as proposed

  11. Chaos Versus Noisy Periodicity: Alternative Hypotheses for Childhood Epidemics

    NASA Astrophysics Data System (ADS)

    Olsen, L. F.; Schaffer, W. M.

    1990-08-01

    Whereas case rates for some childhood diseases (chickenpox) often vary according to an almost regular annual cycle, the incidence of more efficiently transmitted infections such as measles is more variable. Three hypotheses have been proposed to account for such fluctuations. (i) Irregular dynamics result from random shocks to systems with stable equilibria. (ii) The intrinsic dynamics correspond to biennial cycles that are subject to stochastic forcing. (iii) Aperiodic fluctuations are intrinsic to the epidemiology. Comparison of real world data and epidemiological models suggests that measles epidemics are inherently chaotic. Conversely, the extent to which chickenpox outbreaks approximate a yearly cycle depends inversely on the population size.

  12. How the mainstream limits the spreading of alternative hypotheses

    NASA Astrophysics Data System (ADS)

    Kalenda, Pavel

    2014-05-01

    that prof. Djuric had tried for more than 10 years to publish this article in various peer-reviewed journals. So, prof. Djuric got into the official book (list) of "scientific dissidents" among hundreds of other professors and doctors of science (De Climont 2012). These "scientific dissidents" do not have access to established journals and may possibly publish privately or at best on the web in marginal journals whose list was published by De Climont (2012). Such a marginal journal in the field of geophysics and geology is New Concepts in Global Tectonics. This journal has been established because the current hypothesis about the movement of the continents due to convection currents in the mantle becomes under the weight of new observation quite untenable. 4) Scientific consensus History has known many hypotheses that were accepted as proven truth but later, in the light of new knowledge, they completely failed. - No one has the right to decide which scientific hypotheses will be accepted and which will not get into print. Perhaps the worst situation is in climatology (due to global effects and impacts), when the plenary session of IPCC consensually stated that the current global warming was mainly due to the human activity. References De Climont, J. (2012): The worldwide list of dissident scientists. http://astrojan.hostei.com/droa.htm. Djurič, J. (2006): Unification Of Gravitation And Electromagnetism. http://jovandjuric.tripod.com/ David H. Douglass, John R. Christy, Benjamin D. Pearson and S. Fred Singer (2007): A comparison of tropical temperature trends with model predictions. International Journal of Climatology, Volume 28, Issue 13, 15 November 2008, Pages: 1693-1701. http://onlinelibrary.wiley.com/doi/10.1002/joc.1651/pdf. Einstein, A. : List of scientific publications by Albert Einstein. /wiki/List_of_scientific_publications_by_Albert_Einstein. Kolínský, P., Valenta, J. and Gaždová, R. (2012): Seismicity, groundwater level variations and earth tides in

  13. How the mainstream limits the spreading of alternative hypotheses

    NASA Astrophysics Data System (ADS)

    Kalenda, Pavel

    2014-05-01

    that prof. Djuric had tried for more than 10 years to publish this article in various peer-reviewed journals. So, prof. Djuric got into the official book (list) of "scientific dissidents" among hundreds of other professors and doctors of science (De Climont 2012). These "scientific dissidents" do not have access to established journals and may possibly publish privately or at best on the web in marginal journals whose list was published by De Climont (2012). Such a marginal journal in the field of geophysics and geology is New Concepts in Global Tectonics. This journal has been established because the current hypothesis about the movement of the continents due to convection currents in the mantle becomes under the weight of new observation quite untenable. 4) Scientific consensus History has known many hypotheses that were accepted as proven truth but later, in the light of new knowledge, they completely failed. - No one has the right to decide which scientific hypotheses will be accepted and which will not get into print. Perhaps the worst situation is in climatology (due to global effects and impacts), when the plenary session of IPCC consensually stated that the current global warming was mainly due to the human activity. References De Climont, J. (2012): The worldwide list of dissident scientists. http://astrojan.hostei.com/droa.htm. Djurič, J. (2006): Unification Of Gravitation And Electromagnetism. http://jovandjuric.tripod.com/ David H. Douglass, John R. Christy, Benjamin D. Pearson and S. Fred Singer (2007): A comparison of tropical temperature trends with model predictions. International Journal of Climatology, Volume 28, Issue 13, 15 November 2008, Pages: 1693-1701. http://onlinelibrary.wiley.com/doi/10.1002/joc.1651/pdf. Einstein, A. : List of scientific publications by Albert Einstein. /wiki/List_of_scientific_publications_by_Albert_Einstein. Kolínský, P., Valenta, J. and Gaždová, R. (2012): Seismicity, groundwater level variations and earth tides in

  14. Consider the Alternative: The Effects of Causal Knowledge on Representing and Using Alternative Hypotheses in Judgments under Uncertainty

    ERIC Educational Resources Information Center

    Hayes, Brett K.; Hawkins, Guy E.; Newell, Ben R.

    2016-01-01

    Four experiments examined the locus of impact of causal knowledge on consideration of alternative hypotheses in judgments under uncertainty. Two possible loci were examined; overcoming neglect of the alternative when developing a representation of a judgment problem and improving utilization of statistics associated with the alternative…

  15. Testing Alternative Hypotheses Regarding the Association between Behavioral Inhibition and Language Development in Toddlerhood

    ERIC Educational Resources Information Center

    Watts, Ashley K. Smith; Patel, Deepika; Corley, Robin P.; Friedman, Naomi P.; Hewitt, John K.; Robinson, JoAnn L.; Rhee, Soo H.

    2014-01-01

    Studies have reported an inverse association between language development and behavioral inhibition or shyness across childhood, but the direction of this association remains unclear. This study tested alternative hypotheses regarding this association in a large sample of toddlers. Data on behavioral inhibition and expressive and receptive…

  16. Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence

    PubMed Central

    Collins, Allen G.

    1998-01-01

    Six alternative hypotheses for the phylogenetic origin of Bilateria are evaluated by using complete 18S rRNA gene sequences for 52 taxa. These data suggest that there is little support for three of these hypotheses. Bilateria is not likely to be the sister group of Radiata or Ctenophora, nor is it likely that Bilateria gave rise to Cnidaria or Ctenophora. Instead, these data reveal a close relationship between bilaterians, placozoans, and cnidarians. From this, several inferences can be drawn. Morphological features that previously have been identified as synapomorphies of Bilateria and Ctenophora, e.g., mesoderm, more likely evolved independently in each clade. The endomesodermal muscles of bilaterians may be homologous to the endodermal muscles of cnidarians, implying that the original bilaterian mesodermal muscles were myoepithelial. Placozoans should have a gastrulation stage during development. Of the three hypotheses that cannot be falsified with the 18S rRNA data, one is most strongly supported. This hypothesis states that Bilateria and Placozoa share a more recent common ancestor than either does to Cnidaria. If true, the simplicity of placozoan body architecture is secondarily derived from a more complex ancestor. This simplification may have occurred in association with a planula-type larva becoming reproductive before metamorphosis. If this simplification took place during the common history that placozoans share with bilaterians, then placozoan genes that contain a homeobox, such as Trox2, should be explored, for they may include the gene or genes most closely related to Hox genes of bilaterians. PMID:9860990

  17. Habitat structure mediates predation risk for sedentary prey: Experimental tests of alternative hypotheses

    USGS Publications Warehouse

    Chalfoun, A.D.; Martin, T.E.

    2009-01-01

    Predation is an important and ubiquitous selective force that can shape habitat preferences of prey species, but tests of alternative mechanistic hypotheses of habitat influences on predation risk are lacking. 2. We studied predation risk at nest sites of a passerine bird and tested two hypotheses based on theories of predator foraging behaviour. The total-foliage hypothesis predicts that predation will decline in areas of greater overall vegetation density by impeding cues for detection by predators. The potential-prey-site hypothesis predicts that predation decreases where predators must search more unoccupied potential nest sites. 3. Both observational data and results from a habitat manipulation provided clear support for the potential-prey-site hypothesis and rejection of the total-foliage hypothesis. Birds chose nest patches containing both greater total foliage and potential nest site density (which were correlated in their abundance) than at random sites, yet only potential nest site density significantly influenced nest predation risk. 4. Our results therefore provided a clear and rare example of adaptive nest site selection that would have been missed had structural complexity or total vegetation density been considered alone. 5. Our results also demonstrated that interactions between predator foraging success and habitat structure can be more complex than simple impedance or occlusion by vegetation. ?? 2008 British Ecological Society.

  18. Testing Alternative Hypotheses Regarding the Association Between Behavioral Inhibition and Language Development in Toddlerhood

    PubMed Central

    Watts, Ashley K. Smith; Patel, Deepika; Corley, Robin P.; Friedman, Naomi P.; Hewitt, John K.; Robinson, JoAnn L.; Rhee, Soo H.

    2014-01-01

    Studies have reported an inverse association between language development and behavioral inhibition or shyness across childhood, but the direction of this association is unclear. The present study tested alternative hypotheses regarding this association in a large sample of toddlers. Data on behavioral inhibition and expressive and receptive language abilities were collected from 816 twins at ages 14, 20, and 24 months. Growth and regression models were fit to the data to assess the longitudinal associations between behavioral inhibition and language development from 14 to 24 months. Overall, there were significant associations between behavioral inhibition and expressive language, and minimal associations with receptive language, indicating that the association is better explained by reticence to respond rather than deficient language development. PMID:24499266

  19. Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability

    PubMed Central

    McKechnie, Iain; Lepofsky, Dana; Moss, Madonna L.; Butler, Virginia L.; Orchard, Trevor J.; Coupland, Gary; Foster, Fredrick; Caldwell, Megan; Lertzman, Ken

    2014-01-01

    Pacific herring (Clupea pallasii), a foundation of coastal social-ecological systems, is in decline throughout much of its range. We assembled data on fish bones from 171 archaeological sites from Alaska, British Columbia, and Washington to provide proxy measures of past herring distribution and abundance. The dataset represents 435,777 fish bones, dating throughout the Holocene, but primarily to the last 2,500 y. Herring is the single-most ubiquitous fish taxon (99% ubiquity) and among the two most abundant taxa in 80% of individual assemblages. Herring bones are archaeologically abundant in all regions, but are superabundant in the northern Salish Sea and southwestern Vancouver Island areas. Analyses of temporal variability in 50 well-sampled sites reveals that herring exhibits consistently high abundance (>20% of fish bones) and consistently low variance (<10%) within the majority of sites (88% and 96%, respectively). We pose three alternative hypotheses to account for the disjunction between modern and archaeological herring populations. We reject the first hypothesis that the archaeological data overestimate past abundance and underestimate past variability. We are unable to distinguish between the second two hypotheses, which both assert that the archaeological data reflect a higher mean abundance of herring in the past, but differ in whether variability was similar to or less than that observed recently. In either case, sufficient herring was consistently available to meet the needs of harvesters, even if variability is damped in the archaeological record. These results provide baseline information prior to herring depletion and can inform modern management. PMID:24550468

  20. Alternative hypothese for the origin of the ultra-low velocity zones

    NASA Astrophysics Data System (ADS)

    Li, J.; Liu, J.; Hrubiak, R.; Smith, J.

    2015-12-01

    Decades ago seismic tomography revealed peculiar patches known as the ultra-low-velocity zones (ULVZ), located just above the Earth's core-mantle boundary. Typically 5 to 40 km in height, and 100 km in lateral extent, the ULVZs are denser than the surrounding mantle by about 10%, and slower in shear and compressional wave velocities by roughly 30% and 10%, respectively. Elucidating the origin of ULVZs is a key issue in understanding mantle heterogeneity and unraveling the history of chemical differentiation in deep Earth. Existing models invoking partial melting of silicate lithology require specific solidus temperatures to produce isolated melt regions, and they may not be able to account for the large density excess.The scenarios involving iron-rich post-bridgmanite or ferropericlase have been questioned by recent theoretical results showing that iron enrichment in crystalline phases cannot simultaneously explain the observed density and velocity anomalies. Thus the nature of the ULVZs has remained enigmatic. Here we show that the eutectic melting curve of the iron-carbon binary system intersects with the present-day geotherm near the base of the Earth's mantle, suggesting the presence of metallic melt in the D" layer. Using an established model for solid-liquid compositions and approximate values of density and elastic parameters, we found that introducing a suitable fraction of metallic melt could match all the seismic observations, and the fraction depends on the wetting behavior of the melt. We propose a number of alternative hypotheses for the origin of the ultra-low velocity zones, including short-lived ULVZs with metallic melt that are supplied by subducted slabs, long-lasting ULVZs involving both metallic and silicate melts, and ULVZs containing iron-rich solids and residual metallic melt. These hypotheses can be tested by future studies on surface tension, element partitioning, elastic properties, and dynamic modeling.

  1. Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau.

    PubMed

    Macey, J R; Schulte, J A; Ananjeva, N B; Larson, A; Rastegar-Pouyani, N; Shammakov, S M; Papenfuss, T J

    1998-08-01

    Phylogenetic relationships within the Laudakia caucasia species group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation of Laudakia populations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north-south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5-10 MYBP (million years before present)]. The shortest tree suggest the later hypothesis, and statistical tests reject the other two hypothesis. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north-south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61-0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree. PMID:9751922

  2. Gender Organization of Schooling and Television Viewing among Early Adolescents: A Test of Two Alternative Hypotheses

    ERIC Educational Resources Information Center

    Brutsaert, Herman

    2004-01-01

    In this analysis, single-sex and mixed schools are compared in terms of pupils' television viewing habits, the latter factor being considered as an indicator of a pupil's sense of educational responsibilities. It was hypothesized that the presumably lower levels of television watching among girls attending single-sex schools could be explained by…

  3. Confirmatory and Competitive Evaluation of Alternative Gene-Environment Interaction Hypotheses

    ERIC Educational Resources Information Center

    Belsky, Jay; Pluess, Michael; Widaman, Keith F.

    2013-01-01

    Background: Most gene-environment interaction (GXE) research, though based on clear, vulnerability-oriented hypotheses, is carried out using exploratory rather than hypothesis-informed statistical tests, limiting power and making formal evaluation of competing GXE propositions difficult. Method: We present and illustrate a new regression technique…

  4. Phylogenetics.

    PubMed

    Sleator, Roy D

    2011-04-01

    The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects. PMID:21249334

  5. Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

    PubMed Central

    Ord, Terry J.; Garcia-Porta, Joan

    2012-01-01

    Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

  6. The developmental antecedents of sexual coercion against women: testing alternative hypotheses with structural equation modeling.

    PubMed

    Knight, Raymond A; Sims-Knight, Judith E

    2003-06-01

    A unified model of the origin of sexual aggression against women on both adult and juvenile sexual offender samples has been developed and successfully tested. This model proposed three major causal paths to sexual coercion against women. In the first path, physical and verbal abuse was hypothesized to produce callousness and lack of emotionality, which disinhibited sexual drive and sexual fantasies. These in turn disinhibited hostile sexual fantasies, and led to sexual coercion. In the second causal path, sexual abuse contributed directly to the disinhibition of sexual drive and sexual fantasies, which through hostile sexual fantasies led to sexual coercion. The third path operated through early antisocial behavior, including aggressive acts. It developed as a result of both physical/verbal abuse and callousness/lack of emotion. It in turn directly affected sexual coercion and worked indirectly through the hostile sexual fantasies path. In the present study, the anonymous responses of a group of 168 blue-collar, community males to an inventory (the Multidimensional Assessment of Sex and Aggression) were used in a structural equation model to test the validity of this model. Moreover, this model was pitted against (Malamuth's (1998)) two-path model. Whereas the three-path model had an excellent fit with the data (CFI =.951, RMSEA =.047), the two-path model fit less well (CFI =.857, RMSEA =.079). These results indicate the superiority of the three-path model and suggest that it constitutes a solid, empirically disconfirmable heuristic for the etiology of sexual coercion against women. PMID:12839887

  7. Misregulation of Gene Expression and Sterility in Interspecies Hybrids: Causal Links and Alternative Hypotheses.

    PubMed

    Civetta, Alberto

    2016-05-01

    Understanding the origin of species is of interest to biologist in general and evolutionary biologist in particular. Hybrid male sterility (HMS) has been a focus in studies of speciation because sterility imposes a barrier to free gene flow between organisms, thus effectively isolating them as distinct species. In this review, I focus on the role of differential gene expression in HMS and speciation. Microarray and qPCR assays have established associations between misregulation of gene expression and sterility in hybrids between closely related species. These studies originally proposed disrupted expression of spermatogenesis genes as a causative of sterility. Alternatively, rapid genetic divergence of regulatory elements, particularly as they relate to the male sex (fast-male evolution), can drive the misregulation of sperm developmental genes in the absence of sterility. The use of fertile hybrids (both backcross and F1 progeny) as controls has lent support to this alternative explanation. Differences in gene expression between fertile and sterile hybrids can also be influenced by a pattern of faster evolution of the sex chromosome (fast-X evolution) than autosomes. In particular, it would be desirable to establish whether known X-chromosome sterility factors can act as trans-regulatory drivers of genome-wide patterns of misregulation. Genome-wide expression studies coupled with assays of proxies of sterility in F1 and BC progeny have identified candidate HMS genes but functional assays, and a better phenotypic characterization of sterility phenotypes, are needed to rigorously test how these genes might contribute to HMS. PMID:27025762

  8. A Bayesian Approach for Discriminating Among Alternative Inheritance Hypotheses in Plant Polyploids: The Allotetraploid Origin of Genus Borderea (Dioscoreaceae)

    PubMed Central

    Catalán, Pilar; Segarra-Moragues, José Gabriel; Palop-Esteban, Marisa; Moreno, Carlos; González-Candelas, Fernando

    2006-01-01

    Polyploidy is a common phenomenon occurring in a vast number of land plants. Investigations of patterns of inheritance and the origins of plants (i.e., autopolyploidy vs. allopolyploidy) usually involve cytogenetic and molecular studies of chromosome pairing, chromosome mapping, and marker segregation analysis through experimental crosses and progeny tests. Such studies are missing for most wild species, for which artificial crosses are difficult, not feasible, or unaffordable. We report here a Bayesian method to discriminate between alternative inheritance patterns in the two extant, tetraploid species of the monocot genus Borderea (Dioscoreaceae), which does not involve progeny array tests. Our approach is based on the screening of a large number of SSR genotypes, which were obtained from successful amplifications of 17 microsatellite regions in individuals of both B. chouardii and B. pyrenaica. We tested for tetrasomic vs. disomic modes of inheritance, using the Bayes factor test. Assignment of genotypes under both alternatives could be unequivocally done for 14 and 11 of the 17 studied microsatellite regions in B. chouardii and B. pyrenaica, respectively, totaling 9502 analyzed genotypes. The comparison of posterior probabilities for the two competing hypotheses across the surveyed loci clearly favored a disomic inheritance pattern. Linkage tests indicated that none of the studied SSR loci were in linkage disequilibrium, thus representing independent samples of the Borderea genome. These results, along with previous allozyme data, support the allotetraploid origin of this paleoendemic genus and reveal the lowest reported chromosome base number for the family of the yams. PMID:16322527

  9. A molecular test of alternative hypotheses of tetraodontiform (Acanthomorpha: Tetraodontiformes) sister group relationships using data from the RAG1 gene.

    PubMed

    Holcroft, Nancy I

    2004-09-01

    Two primary competing hypotheses regarding the identity of the sister group of the order Tetraodontiformes exist. The first hypothesis holds that some or all acanthuroid fishes represent the sister of Tetraodontiformes. The second, proposed in 1984 by Rosen, holds that the order Zeiformes is sister to Tetraodontiformes and that the family Caproidae is sister to this Zeiformes + Tetraodontiformes clade. These two hypotheses were tested using data from the single-copy nuclear gene RAG1. Representatives of most major orders of acanthomorph fishes were included to provide an appropriate context in which to place Tetraodontiformes and its hypothesized sister groups. The results of an unweighted parsimony analysis indicate that Zeiformes is not the sister group of Tetraodontiformes. In addition, Caproidae appears unrelated to Zeiformes. A monophyletic Tetraodontiformes was recovered as the sister group of the clade Ephippidae + Drepanidae and was more distantly related to the included zeiform and caproid representatives. PMID:15288052

  10. The complete mitochondrial genome of the enigmatic bigheadedturtle (Platysternon): description of unusual genomic features and thereconciliation of phylogenetic hypotheses based on mitochondrial andnuclear DNA

    SciTech Connect

    Parham, James F.; Feldman, Chris R.; Boore, Jeffrey L.

    2005-12-28

    The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis. We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles. Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mt DNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded

  11. Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes.

    PubMed

    Mank, Judith E; Avise, John C

    2006-06-01

    Using comparative phylogenetic analysis, we analyzed the evolution of male alternative reproductive tactics (MARTs) in ray-finned fishes (Actinopterygii). Numerous independent origins for each type of MART (involving sneaker males, female mimics, pirates, and satellite males) indicate that these behaviors have been highly labile across actinopterygiian evolution, consistent with a previous notion that convergent selection in fishes can readily mold the underlying suites of reproductive hormones into similar behaviors. The evolutionary appearance of MARTs was significantly correlated with the presence of sexually selected traits in bourgeois males (P = 0.001) but not with the presence of male parental care. This suggests that MARTs often arise from selection on some males to circumvent bourgeois male investment in mate monopolization, rather than to avoid male brood care per se. We found parsimony evidence for an evolutionary progression of MARTs wherein sneaking is usually the evolutionary precursor to the presumably more complex MARTs of female mimicry and cooperative satellite behavior. Nest piracy appears not to be part of this evolutionary progression, possibly because its late onset in the life cycle of most ray-finned fishes reduces the effects of selection on this reproductive tactic. PMID:16892981

  12. Molecular Evolution of Alternative Oxidase Proteins: A Phylogenetic and Structure Modeling Approach.

    PubMed

    Pennisi, Rosa; Salvi, Daniele; Brandi, Valentina; Angelini, Riccardo; Ascenzi, Paolo; Polticelli, Fabio

    2016-05-01

    Alternative oxidases (AOXs) are mitochondrial cyanide-resistant membrane-bound metallo-proteins catalyzing the oxidation of ubiquinol and the reduction of oxygen to water bypassing two sites of proton pumping, thus dissipating a major part of redox energy into heat. Here, the structure of Arabidopsis thaliana AOX 1A has been modeled using the crystal structure of Trypanosoma brucei AOX as a template. Analysis of this model and multiple sequence alignment of members of the AOX family from all kingdoms of Life indicate that AOXs display a high degree of conservation of the catalytic core, which is formed by a four-α-helix bundle, hosting the di-iron catalytic site, and is flanked by two additional α-helices anchoring the protein to the membrane. Plant AOXs display a peculiar covalent dimerization mode due to the conservation in the N-terminal region of a Cys residue forming the inter-monomer disulfide bond. The multiple sequence alignment has also been used to infer a phylogenetic tree of AOXs whose analysis shows a polyphyletic origin for the AOXs found in Fungi and a monophyletic origin of the AOXs of Eubacteria, Mycetozoa, Euglenozoa, Metazoa, and Land Plants. This suggests that AOXs evolved from a common ancestral protein in each of these kingdoms. Within the Plant AOX clade, the AOXs of monocotyledon plants form two distinct clades which have unresolved relationships relative to the monophyletic clade of the AOXs of dicotyledonous plants. This reflects the sequence divergence of the N-terminal region, probably due to a low selective pressure for sequence conservation linked to the covalent homo-dimerization mode. PMID:27090422

  13. Patterns and processes in complex landscapes: testing alternative biogeographical hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i.

    PubMed

    Eldon, Jon; Price, Jonathan P; Magnacca, Karl; Price, Donald K

    2013-07-01

    The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age and geographical isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study, we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet-forest-restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that probably reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographical model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographical systems. PMID:23683316

  14. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons

    PubMed Central

    Minovitsky, Simon; Gee, Sherry L.; Schokrpur, Shiruyeh; Dubchak, Inna; Conboy, John G.

    2005-01-01

    Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is phylogenetically and spatially conserved in introns that flank brain-enriched alternative exons from fish to man. Analysis of sequence from the mouse, rat, dog, chicken and pufferfish genomes revealed a strongly statistically significant association of UGCAUG with the proximal intron region downstream of brain-enriched alternative exons. The number, position and sequence context of intronic UGCAUG elements were highly conserved among mammals and in chicken, but more divergent in fish. Control datasets, including constitutive exons and non-tissue-specific alternative exons, exhibited a much lower incidence of closely linked UGCAUG elements. We propose that the high sequence specificity of the UGCAUG element, and its unique association with tissue-specific alternative exons, mark it as a critical component of splicing switch mechanism(s) designed to activate a limited repertoire of splicing events in cell type-specific patterns. We further speculate that highly conserved UGCAUG-binding protein(s) related to the recently described Fox-1 splicing factor play a critical role in mediating this specificity. PMID:15691898

  15. ISOLATION AND PHYLOGENETIC ANALYSIS OF XYLELLA FASTIDIOSA FROM ITS INVASIVE ALTERNATIVE HOST, PORCELAIN BERRY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A strain of X. fastidiosa was isolated from an invasive alternative host species, porcelain berry. Its genetic relationship with strains isolated from a native alternative host, wild grape, and other economically important hosts including grape, peach, plum, oak, mulberry, maple and oleander was det...

  16. Molecular cloning of large alternative transcripts based on comparative phylogenetic analysis and exploration of an EST database.

    PubMed

    Ji, Jiabing; Wang, Rongfu

    2012-05-15

    In animals, a gene may be 50 kb or over and contain multiple alternative transcripts with sequences that are not experimentally validated. Under these special circumstances, PCR-based cloning may become very difficult. Here a simple cloning strategy is described using the mNLRC5 gene as an example. We performed comparative phylogenetic analysis between murine and human NLR protein families to anchor the translation start codon, searched an EST database with the 3' end of the genomic DNA sequence to obtain ESTs from the farthest 3' end of the gene, and isolated the full-length CDS of the mNLRC5 of about 6 kb through conventional RT-PCR and 3' RACE. PMID:22387390

  17. Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements.

    PubMed

    Seger, G D S; Duarte, L D S; Debastiani, V J; Kindel, A; Jarenkow, J A

    2013-09-01

    Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure. PMID:23368095

  18. Testing New Hypotheses Regarding Ebolavirus Reservoirs

    PubMed Central

    Leendertz, Siv Aina Jensen

    2016-01-01

    Despite a relatively long search for the origin of ebolaviruses, their reservoirs remain elusive. Researchers might have to consider testing alternative hypotheses about how these viruses persist and emerge to advance ebolavirus research. This article aims to encourage researchers to bring forward such hypotheses, to discuss them scientifically and to open alternative research avenues regarding the origin and ecology of ebolaviruses.

  19. Unleashing the force of cladistics? Metazoan phylogenetics and hypothesis testing.

    PubMed

    Jenner, Ronald A

    2003-02-01

    The accumulation of multiple phylogenetic hypotheses for the Metazoa invites an evaluation of current progress in the field. I discuss three case studies from the recent literature to assess how cladistic analyses of metazoan morphology have contributed to our understanding of animal evolution. The first case study on cleavage cross patterns examines whether a decade of unanimous character scoring across different cladistic studies can be considered a reliable indicator of accumulated wisdom. The two remaining case studies illustrate how the unique strength of cladistic analyses to arbitrate between competing hypotheses can be crippled when insufficient attention is directed towards the construction of the data matrix. The second case study discusses a recent morphological cladistic analysis aimed at providing insight into the evolution of larval ciliary bands (prototrochs) in the Spiralia, and the third case study evaluates how four subsequent morphological cladistic analyses have contributed to our understanding of the phylogenetic placement of a problematicum, the Myzostomida. I conclude that current phylogenetic analyses of the Metazoa have not fully exploited the power of cladistics to test available alternative hypotheses. If our goal is to generate genuine progress in understanding rather than stochastic variation of opinions through time, we have to shift our attention from using cladistics as an easy tool to generate "novel" hypotheses of metazoan relationships, towards employing cladistics more critically as an effective instrument to test the relative merit of available multiple alternative hypotheses. PMID:21680424

  20. Phylogenetic analysis of ligninolytic peroxidases: preliminary insights into the alternation of white-rot and brown-rot fungi in their lineage.

    PubMed

    Zhou, Li-Wei; Wei, Yu-Lian; Dai, Yu-Cheng

    2014-03-01

    White-rot and brown-rot fungi employ different mechanisms to degrade lignocellulose. These fungi are not monophyletic and even alternate in their common lineage. To explore the reason for this, seventy-six ligninolytic peroxidases (LPs), including 14 sequences newly identified from available basidiomycetous whole-genome and EST databases in this study, were utilized for phylogenetic and selective pressure analyses. We demonstrate that LPs were subjected to the mixed process of concerted and birth-and-death evolution. After the duplication events of original LPs, various LP types may originate from mutation events of several key residues driven by positive selection, which may change LP types and even rot types in a small fraction of wood-decaying fungi. Our findings provide preliminary insights into the cause for the alternation of the two fungal rot types within the same lineage. PMID:24772372

  1. Phylogenetic analysis of ligninolytic peroxidases: preliminary insights into the alternation of white-rot and brown-rot fungi in their lineage

    PubMed Central

    Zhou, Li-Wei; Wei, Yu-Lian; Dai, Yu-Cheng

    2014-01-01

    White-rot and brown-rot fungi employ different mechanisms to degrade lignocellulose. These fungi are not monophyletic and even alternate in their common lineage. To explore the reason for this, seventy-six ligninolytic peroxidases (LPs), including 14 sequences newly identified from available basidiomycetous whole-genome and EST databases in this study, were utilized for phylogenetic and selective pressure analyses. We demonstrate that LPs were subjected to the mixed process of concerted and birth-and-death evolution. After the duplication events of original LPs, various LP types may originate from mutation events of several key residues driven by positive selection, which may change LP types and even rot types in a small fraction of wood-decaying fungi. Our findings provide preliminary insights into the cause for the alternation of the two fungal rot types within the same lineage. PMID:24772372

  2. Testing Alternative Hypotheses about Animal Behavior.

    ERIC Educational Resources Information Center

    Baker, William P.; Lang, Michael; Lawson, Anton E.

    Research indicates that the effectiveness of instruction in the elementary classroom is enhanced when it incorporates materials that actively engage students in the generation of scientific explanations. To this end, this document describes an exercise that allows Kindergarten students to explore the basic principles of animal behavior in an…

  3. Perceptions as Hypotheses

    NASA Astrophysics Data System (ADS)

    Gregory, R. L.

    1980-07-01

    Perceptions may be compared with hypotheses in science. The methods of acquiring scientific knowledge provide a working paradigm for investigating processes of perception. Much as the information channels of instruments, such as radio telescopes, transmit signals which are processed according to various assumptions to give useful data, so neural signals are processed to give data for perception. To understand perception, the signal codes and the stored knowledge or assumptions used for deriving perceptual hypotheses must be discovered. Systematic perceptual errors are important clues for appreciating signal channel limitations, and for discovering hypothesis-generating procedures. Although this distinction between `physiological' and `cognitive' aspects of perception may be logically clear, it is in practice surprisingly difficult to establish which are responsible even for clearly established phenomena such as the classical distortion illusions. Experimental results are presented, aimed at distinguishing between and discovering what happens when there is mismatch with the neural signal channel, and when neural signals are processed inappropriately for the current situation. This leads us to make some distinctions between perceptual and scientific hypotheses, which raise in a new form the problem: What are `objects'?

  4. Phylogenetic comparison of the pre-mRNA adenosine deaminase ADAR2 genes and transcripts: conservation and diversity in editing site sequence and alternative splicing patterns.

    PubMed

    Slavov, D; Gardiner, K

    2002-10-16

    Adenosine deaminase that acts on RNA -2 (ADAR2) is a member of a family of vertebrate genes that encode adenosine (A)-to-inosine (I) RNA deaminases, enzymes that deaminate specific A residues in specific pre-mRNAs to produce I. Known substrates of ADAR2 include sites within the coding regions of pre-mRNAs of the ionotropic glutamate receptors, GluR2-6, and the serotonin receptor, 5HT2C. Mammalian ADAR2 expression is itself regulated by A-to-I editing and by several alternative splicing events. Because the biological consequences of ADAR2 function are significant, we have undertaken a phylogenetic comparison of these features. Here we report a comparison of cDNA sequences, genomic organization, editing site sequences and patterns of alternative splicing of ADAR2 genes from human, mouse, chicken, pufferfish and zebrafish. Coding sequences and intron/exon organization are highly conserved. All ADAR2 genes show evidence of transcript editing with required sequences and predicted secondary structures very highly conserved. Patterns and levels of editing and alternative splicing vary among organisms, and include novel N-terminal exons and splicing events. PMID:12459255

  5. The ipdC, hisC1 and hisC2 genes involved in indole-3-acetic production used as alternative phylogenetic markers in Azospirillum brasilense.

    PubMed

    Jijón-Moreno, Saúl; Marcos-Jiménez, Cynthia; Pedraza, Raúl O; Ramírez-Mata, Alberto; de Salamone, I García; Fernández-Scavino, Ana; Vásquez-Hernández, Claudia A; Soto-Urzúa, Lucia; Baca, Beatriz E

    2015-06-01

    Plant growth-promoting bacteria of the genus Azospirillum are present in the rhizosphere and as endophytes of many crops. In this research we studied 40 Azospirillum strains isolated from different plants and geographic regions. They were first characterized by 16S rDNA restriction analysis, and their phylogenetic position was established by sequencing the genes 16S rDNA, ipdC, hisC1, and hisC2. The latter three genes are involved in the indole-3-pyruvic acid (IPyA) biosynthesis pathway of indole-3-acetic acid (IAA). Furthermore, the suitability of the 16S-23S rDNA intergenic spacer sequence (IGS) for the differentiation of closely related Azospirillum taxa and development of PCR protocols allows for specific detection of strains. The IGS-RFLP analysis enabled intraspecies differentiation, particularly of Azospirillum brasilense and Azospirillum lipoferum strains. Results demonstrated that the ipdC, hisC1, and hisC2 genes are highly conserved in all the assessed A. brasilense isolates, suggesting that these genes can be used as an alternative phylogenetic marker. In addition, IAA production determined by HPLC ranged from 0.17 to 98.2 μg mg(-1) protein. Southern hybridization with the A. brasilense ipdC gene probe did not show, a hybridization signal with A. lipoferum, Azospirillum amazonense, Azospirillum halopreferans and Azospirillum irakense genomic DNA. This suggests that these species produce IAA by other pathways. Because IAA is mainly synthesized via the IPyA pathway in A. brasilense strains, a species that is used worldwide in agriculture, the identification of ipdC, hisC1, and hisC2 genes by PCR may be suitable for selecting exploitable strains. PMID:25842039

  6. Testing hypotheses in macroevolution.

    PubMed

    Bromham, Lindell

    2016-02-01

    Experimental manipulation of microevolution (changes in frequency of heritable traits in populations) has shed much light on evolutionary processes. But many evolutionary processes occur on scales that are not amenable to experimental manipulation. Indeed, one of the reasons that macroevolution (changes in biodiversity over time, space and lineages) has sometimes been a controversial topic is that processes underlying the generation of biological diversity generally operate at scales that are not open to direct observation or manipulation. Macroevolutionary hypotheses can be tested by using them to generate predictions then asking whether observations from the biological world match those predictions. Each study that identifies significant correlations between evolutionary events, processes or outcomes can generate new predictions that can be further tested with different datasets, allowing a cumulative process that may narrow down on plausible explanations, or lead to rejection of other explanations as inconsistent or unsupported. A similar approach can be taken even for unique events, for example by comparing patterns in different regions, lineages, or time periods. I will illustrate the promise and pitfalls of these approaches using a range of examples, and discuss the problems of inferring causality from significant evolutionary associations. PMID:26774069

  7. Are mimics monophyletic? The necessity of phylogenetic hypothesis tests in character evolution

    PubMed Central

    2010-01-01

    Background The processes governing the origin and maintenance of mimetic phenotypes can only be understood in a phylogenetic framework. Phylogenetic estimates of evolutionary relationships can provide a context for analyses of character evolution; however, when phylogenetic estimates conflict, rigorous analyses of alternative evolutionary histories are necessary to determine the likelihood of a specific history giving rise to the observed pattern of diversity. The polyphenic butterfly Limenitis arthemis provides a case in point. This species is comprised of three lineages, two of which are mimetic and one of which is non-mimetic. Conflicting estimates of the relationships among these three lineages requires direct evaluation of the alternative hypotheses of mimicry evolution. Results Using a coalescent framework, we found support for a sister-taxon relationship between the non-mimetic L. a. arthemis and the mimetic L. a. astyanax, congruent with the previous hypothesis that the non-mimetic form of L. a. arthemis was derived from a mimetic ancestor. We found no support for a mimetic clade (L. a. astyanax + L. a. arizonensis) despite analyzing numerous models of population structure. Conclusions These results provide the foundation for future studies of mimicry, which should integrate phylogenetic and developmental analyses of wing pattern formation. We propose future analyses of character evolution accommodate conflicting phylogenetic estimates by explicitly testing alternative evolutionary hypotheses. PMID:20682073

  8. Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens.

    PubMed

    Keck, Benjamin P; Hulsey, C Darrin

    2014-04-01

    The incredibly species-rich cichlid fish faunas of both the Neotropics and Africa are generally thought to be reciprocally monophyletic. However, the phylogenetic affinity of the African cichlid Heterochromis multidens is ambiguous, and this distinct lineage could make African cichlids paraphyletic. In past studies, Heterochromis has been variously suggested to be one of the earliest diverging lineages within either the Neotropical or the African cichlid radiations, and it has even been hypothesized to be the sister lineage to a clade containing all Neotropical and African cichlids. We examined the phylogenetic relationships among a representative sample of cichlids with a dataset of 29 nuclear loci to assess the support for the different hypotheses of the phylogenetic position of Heterochromis. Although individual gene trees in some instances supported alternative relationships, a majority of gene trees, integration of genes into species trees, and hypothesis testing of putative topologies all supported Heterochromis as belonging to the clade of African cichlids. PMID:24472673

  9. The more, the better: the use of multiple landmark configurations to solve the phylogenetic relationships in musteloids.

    PubMed

    Catalano, Santiago A; Ercoli, Marcos D; Prevosti, Francisco J

    2015-03-01

    Although the use of landmark data to study shape changes along a phylogenetic tree has become a common practice in evolutionary studies, the role of this sort of data for the inference of phylogenetic relationships remains under debate. Theoretical issues aside, the very existence of historical information in landmark data has been challenged, since phylogenetic analyses have often shown little congruence with alternative sources of evidence. However, most analyses conducted in the past were based upon a single landmark configuration, leaving it unsettled whether the incorporation of multiple configurations may improve the rather poor performance of this data source in most previous phylogenetic analyses. In the present study, we present a phylogenetic analysis of landmark data that combines information derived from several skeletal structures to derive a phylogenetic tree for musteloids. The analysis includes nine configurations representing different skeletal structures for 24 species. The resulting tree presents several notable concordances with phylogenetic hypotheses derived from molecular data. In particular, Mephitidae, Procyonidae, and Lutrinae plus the genera Martes, Mustela, Galictis, and Procyon were retrieved as monophyletic. In addition, other groupings were in agreement with molecular phylogenies or presented only minor discordances. Complementary analyses have also indicated that the results improve substantially when an increasing number of landmark configurations are included in the analysis. The results presented here thus highlight the importance of combining information from multiple structures to derive phylogenetic hypotheses from landmark data. PMID:25516268

  10. The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura).

    PubMed

    Bittencourt-Silva, Gabriela B; Conradie, Werner; Siu-Ting, Karen; Tolley, Krystal A; Channing, Alan; Cunningham, Michael; Farooq, Harith M; Menegon, Michele; Loader, Simon P

    2016-06-01

    The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group. PMID:27001603

  11. [Foundations of the new phylogenetics].

    PubMed

    Pavlinov, I Ia

    2004-01-01

    Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into

  12. Refuting phylogenetic relationships

    PubMed Central

    Bucknam, James; Boucher, Yan; Bapteste, Eric

    2006-01-01

    Background Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny. Results We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity of N. equitans and the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes. Conclusion It is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers. Reviewers This article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten. PMID:16956399

  13. Amerind taxonomy and testable hypotheses.

    PubMed

    Pichardo, M

    1998-06-01

    The acceptance of a 30,000 yr B.P. age for Valsequillo sets new parameters for hypotheses of Paleoindian entry into America. A review of Amerind taxonomy defines the early groups as Otamid-Sundadonts. Isolation in America led to an adaptive radiation that has implications for the origin and dispersal of Pithecanthropus. PMID:9653503

  14. Phylogenetic signal dissection identifies the root of starfishes.

    PubMed

    Feuda, Roberto; Smith, Andrew B

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  15. Phylogenetic Signal Dissection Identifies the Root of Starfishes

    PubMed Central

    Feuda, Roberto; Smith, Andrew B.

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  16. Testing hypotheses of earthquake occurrence

    NASA Astrophysics Data System (ADS)

    Kagan, Y. Y.; Jackson, D. D.; Schorlemmer, D.; Gerstenberger, M.

    2003-12-01

    We present a relatively straightforward likelihood method for testing those earthquake hypotheses that can be stated as vectors of earthquake rate density in defined bins of area, magnitude, and time. We illustrate the method as it will be applied to the Regional Earthquake Likelihood Models (RELM) project of the Southern California Earthquake Center (SCEC). Several earthquake forecast models are being developed as part of this project, and additional contributed forecasts are welcome. Various models are based on fault geometry and slip rates, seismicity, geodetic strain, and stress interactions. We would test models in pairs, requiring that both forecasts in a pair be defined over the same set of bins. Thus we offer a standard "menu" of bins and ground rules to encourage standardization. One menu category includes five-year forecasts of magnitude 5.0 and larger. Forecasts would be in the form of a vector of yearly earthquake rates on a 0.05 degree grid at the beginning of the test. Focal mechanism forecasts, when available, would be also be archived and used in the tests. The five-year forecast category may be appropriate for testing hypotheses of stress shadows from large earthquakes. Interim progress will be evaluated yearly, but final conclusions would be made on the basis of cumulative five-year performance. The second category includes forecasts of earthquakes above magnitude 4.0 on a 0.05 degree grid, evaluated and renewed daily. Final evaluation would be based on cumulative performance over five years. Other types of forecasts with different magnitude, space, and time sampling are welcome and will be tested against other models with shared characteristics. All earthquakes would be counted, and no attempt made to separate foreshocks, main shocks, and aftershocks. Earthquakes would be considered as point sources located at the hypocenter. For each pair of forecasts, we plan to compute alpha, the probability that the first would be wrongly rejected in favor of

  17. Molecular Phylogenetic Information on the Identity of the Closest Living Relative(s) of Land Vertebrates

    NASA Astrophysics Data System (ADS)

    Zardoya, Rafael; Meyer, Axel

    The phylogenetic position of tetrapods relative to the other two living sarcopterygian lineages (lungfishes and the coelacanth) has been subject to debate for many decades, yet remains unresolved. There are three possible alternatives for the phylogenetic relationships among these three living lineages of sarcopterygians, i.e., lungfish as living sister group of tetrapods, the coelacanth as closest living relative of tetrapods, and lungfish and coelacanth equally closely related to tetrapods. To resolve this important evolutionary question several molecular data sets have been collected in recent years, the largest being the almost complete 28S rRNA gene sequences (about 3500bp) and the complete mitochondrial genomes of the coelacanth and a lungfish (about 16500bp each). Phylogenetic analyses of several molecular data sets had not provided unequivocal support for any of the three hypotheses. However, a lungfish+tetrapod or a lungfish+coelacanth clade were predominantly favored over a coelacanth+tetrapod grouping when the entire mitochondrial genomes alone or in combination with the nuclear 28S rRNA gene data were analyzed with maximum parsimony, neighbor-joining, and maximum likelihood phylogenetic methods. Also, current paleontological and morphological data seem to concur with these molecular results. Therefore the currently available molecular data seems to rule out a coelacanth+tetrapod relationship, the traditional textbook hypothesis. These tentative molecular phylogenetic results point to the inherent difficulty in resolving relationships among lineages which apparently originated in rapid succession during the Devonian.

  18. Nigeria`s oil production behavior: Tests of alternative hypotheses

    SciTech Connect

    Awokuse, T.O.; Jones, C.T.

    1994-12-31

    The sudden quadrupling of world oil prices in 1973-1974 marked the beginning of several formal inquiries by economists into the production behavior of members of the Organization of the Petroleum Exporting Countries (OPEC). Interest in the organization was further heightened in 1979 when nominal oil prices further doubled. However, oil market analysts have differed in their evaluation of OPEC`s role in the determination of world oil prices. Most energy economists have modeled OPEC as a cartel. Morris Adelman has suggested that OPEC`s true nature lies somewhere between two polar cases of a dominant-firm industry and an imperfect, market-sharing cartel. In the former case, one large, dominant firm (i.e., Saudi Arabia) serves as the {open_quotes}swing producer,{close_quotes} allowing other cartel members and non-OPEC oil producers to produce whatever they wished, controlling the market price by itself through its own output adjustments. The latter case of an imperfect market-sharing cartel is a loose collusive arrangement in which all members agree on an acceptable price level and individual output shares for each producer. Adelman believes that OPEC wobbles between these two cases, depending upon market conditions.

  19. How does cognition evolve? Phylogenetic comparative psychology

    PubMed Central

    Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

    2014-01-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

  20. Deficiency in the Opioid Hypotheses of Self-Injurious Behavior.

    ERIC Educational Resources Information Center

    King, Bryan H.; And Others

    1991-01-01

    This commentary critiques two papers by Curt Sandman, pointing out interpretive problems in models explaining self-injurious behavior in terms of opioids. Withdrawal effects are emphasized as an alternative to hypotheses asserting congenital opioid excess as a cause of sensory depression or an addiction to a relative excess of opioid activity in…

  1. Phylogenetic analysis of adenovirus sequences.

    PubMed

    Harrach, Balázs; Benko, Mária

    2007-01-01

    Members of the family Adenoviridae have been isolated from a large variety of hosts, including representatives from every major vertebrate class from fish to mammals. The high prevalence, together with the fairly conserved organization of the central part of their genomes, make the adenoviruses one of (if not the) best models for studying viral evolution on a larger time scale. Phylogenetic calculation can infer the evolutionary distance among adenovirus strains on serotype, species, and genus levels, thus helping the establishment of a correct taxonomy on the one hand, and speeding up the process of typing new isolates on the other. Initially, four major lineages corresponding to four genera were recognized. Later, the demarcation criteria of lower taxon levels, such as species or types, could also be defined with phylogenetic calculations. A limited number of possible host switches have been hypothesized and convincingly supported. Application of the web-based BLAST and MultAlin programs and the freely available PHYLIP package, along with the TreeView program, enables everyone to make correct calculations. In addition to step-by-step instruction on how to perform phylogenetic analysis, critical points where typical mistakes or misinterpretation of the results might occur will be identified and hints for their avoidance will be provided. PMID:17656792

  2. RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa.

    PubMed

    Herrera, Santiago; Shank, Timothy M

    2016-07-01

    Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness are particularly problematic. In this study, we demonstrate the utility of restriction site associated DNA sequencing (RAD-seq) to objectively resolve unambiguous phylogenetic relationships in a recalcitrant group of deep-sea corals with divergences >80 million years. We infer robust species boundaries in the genus Paragorgia by testing alternative delimitation hypotheses using a Bayes Factors delimitation method. We present substantial evidence rejecting the current morphological species delimitation model for the genus and infer the presence of cryptic species associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences cannot be assessed in terms of absolute time, but are contingent on taxon-specific factors. We show that classical taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypotheses. Our results lead the way for addressing further questions in marine biogeography, community ecology, population dynamics, conservation, and evolution. PMID:26993764

  3. Global Biodiversity and Phylogenetic Evaluation of Remipedia (Crustacea)

    PubMed Central

    Neiber, Marco T.; Hartke, Tamara R.; Stemme, Torben; Bergmann, Alexandra; Rust, Jes; Iliffe, Thomas M.; Koenemann, Stefan

    2011-01-01

    Remipedia is one of the most recently discovered classes of crustaceans, first described in 1981 from anchialine caves in the Bahamas Archipelago. The class is divided into the order Enantiopoda, represented by two fossil species, and Nectiopoda, which contains all known extant remipedes. Since their discovery, the number of nectiopodan species has increased to 24, half of which were described during the last decade. Nectiopoda exhibit a disjunct global distribution pattern, with the highest abundance and diversity in the Caribbean region, and isolated species in the Canary Islands and in Western Australia. Our review of Remipedia provides an overview of their ecological characteristics, including a detailed list of all anchialine marine caves, from which species have been recorded. We discuss alternative hypotheses of the phylogenetic position of Remipedia within Arthropoda, and present first results of an ongoing molecular-phylogenetic analysis that do not support the monophyly of several nectiopodan taxa. We believe that a taxonomic revision of Remipedia is absolutely essential, and that a comprehensive revision should include a reappraisal of the fossil record. PMID:21625553

  4. Furious Frederich: Nietzsche's neurosyphilis diagnosis and new hypotheses.

    PubMed

    André, Charles; Rios, André Rangel

    2015-12-01

    The causes of Friedrich Nietzsche's mental breakdown in early 1889 and of the subsequent slow decay to end-stage dementia along ten years will possibly remain open to debate. The diagnosis of syphilitic dementia paralytica, based only on medical anamnesis and physical examination, was considered indisputable by Otto Binswanger. On the other hand, taking into account recently described diseases, selectively collected evidence lend some support to alternative hypotheses: basal forebrain meningioma, CADASIL, MELAS and frontotemporal dementia. PMID:26465288

  5. Cnidarian phylogenetic relationships as revealed by mitogenomics

    PubMed Central

    2013-01-01

    Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

  6. Exploring hypotheses in attitude control fault diagnosis

    NASA Technical Reports Server (NTRS)

    Bell, Benjamin

    1987-01-01

    A system which analyzes telemetry and evaluates hypotheses to explain any anomalies that are observed is described. Results achieved from a sample set of failure cases are presented, followed by a brief discussion of the benefits derived from this approach.

  7. Teaching Rival Hypotheses in Experimental Psychology.

    ERIC Educational Resources Information Center

    Howard, George S.; Engelhardt, Jean L.

    1984-01-01

    Students critiqued research contained in the book "Rival Hypotheses" (Huck and Sandler, 1979), which contains studies dealing with knowledge claims of practical importance, e.g., the evidence that saccharine causes cancer. (RM)

  8. Is PDGF really important? Testing the hypotheses.

    PubMed

    Bowen-Pope, D F; van Koppen, A; Schatteman, G

    1991-01-01

    Platelet-derived growth factor (PDGF) has been proposed to be one of the growth factors that drive proliferation during normal development and in various pathological conditions. Support for these hypotheses has been largely circumstantial. We discuss the pros and cons of the different experimental approaches that have been taken to test these hypotheses, and evaluate the information to be gained by characterizing the consequences of deletion of one of the PDGF receptor genes in the Patch mutant mouse. PMID:1668194

  9. Nearly Complete 28S rRNA Gene Sequences Confirm New Hypotheses of Sponge Evolution

    PubMed Central

    Thacker, Robert W.; Hill, April L.; Hill, Malcolm S.; Redmond, Niamh E.; Collins, Allen G.; Morrow, Christine C.; Spicer, Lori; Carmack, Cheryl A.; Zappe, Megan E.; Pohlmann, Deborah; Hall, Chelsea; Diaz, Maria C.; Bangalore, Purushotham V.

    2013-01-01

    The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges. PMID:23748742

  10. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution.

    PubMed

    Thacker, Robert W; Hill, April L; Hill, Malcolm S; Redmond, Niamh E; Collins, Allen G; Morrow, Christine C; Spicer, Lori; Carmack, Cheryl A; Zappe, Megan E; Pohlmann, Deborah; Hall, Chelsea; Diaz, Maria C; Bangalore, Purushotham V

    2013-09-01

    The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges. PMID:23748742

  11. Phylogenetic lineages in Entomophthoromycota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Entomophthoromycota Humber is one of five major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular st...

  12. Under the Skin: On the Impartial Treatment of Genetic and Environmental Hypotheses of Racial Differences

    ERIC Educational Resources Information Center

    Rowe, David C.

    2005-01-01

    Environmental and genetic explanations have been given for Black-White racial differences in intelligence and other traits. In science, viable, alternative hypotheses are ideally given equal Bayesian prior weights; but this has not been true in the study of racial differences. This article advocates testing environmental and genetic hypotheses of…

  13. Phylogenetic perspectives in the evolution of parental care in ray-finned fishes.

    PubMed

    Mank, Judith E; Promislow, Daniel E L; Avise, John C

    2005-07-01

    Among major vertebrate groups, ray-finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray-finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray-finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female-internal fertilization and gestation. No clear indication emerged that female-only care or biparental care were evolutionary outgrowths of male-only care, or that biparental care

  14. Formative Assessment Probes: To Hypothesize or Not

    ERIC Educational Resources Information Center

    Keeley, Page

    2010-01-01

    Formative assessment probes are used not only to uncover the ideas students bring to their learning, they can also be used to reveal teachers' common misconceptions. Consider a process widely used in inquiry science--developing hypotheses. In this article, the author features the probe "Is It a Hypothesis?", which serves as an example of how…

  15. The status of platyrrhine phylogeny: a meta-analysis and quantitative appraisal of topological hypotheses.

    PubMed

    Perez, S Ivan; Rosenberger, Alfred L

    2014-11-01

    Phylogenetic or species trees reflect the branching process of lineages and have direct and indirect interest for several branches of evolutionary anthropology. Estimating phylogenetic trees is a necessary first step toward understanding the factors responsible for the ecological and phenotypic diversification of a primate clade. The platyrrhines have become well known as a phylogenetic challenge. Since the 1990s, platyrrhine phylogenetic studies have increasingly analyzed DNA sequences, or other molecular datasets. Several researchers have claimed with confidence that platyrrhine phylogenetic history has been 'resolved' using these molecular data, but the concordance among these studies has never been quantified. Here, we perform a meta-analysis of published platyrrhine trees using topological information and multivariate methods. Specifically, we examine the claim that platyrrhine phylogeny has been determined and explore the relationships between phylogenies and dataset types used for phylogenetic inference (nuclear DNA, mtDNA, Alu sequences, morphology or mixed data). We compare topologies summarizing 31 major neontological studies of the platyrrhines produced since 1975. The analysis reveals that major disparities are rather common among the hypotheses regarding the higher-level relationships of platyrrhines. We also find that the global concordance that appears to emerge at the generic level is less impressive when one looks more finely at particular relationships. Moreover, correspondence among trees appears to be related to the 'type' of dataset analyzed, which suggests that the biological properties of distinct datasets have an inherent influence on the likelihood of producing similar reconstructions of phylogenetic relationships. This serves to remind us that the main questions surrounding the phylogeny reconstruction program begin with experimental design, for both molecular and morphological datasets. Thus, previous claims that platyrrhine genus

  16. Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma.

    PubMed

    Kimball, R T; Braun, E L; Ligon, J D

    1997-10-22

    Afropavo congensis, the Congo peafowl, has long fascinated ornithologists because of its uncertain phylogenetic position and unusual geographic distribution. While some researchers have placed Afropavo as a sister taxon to the true peafowl, Pavo species, others have suggested relationships with the guineafowl or an Old World partridge, Francolinus. These divergent opinions are due, at least in part, to (i) the unique morphological characteristics, lack of elaborate ornamentation, and monogamous mating system in Afropavo which differentiates it from Pavo; and (ii) the restricted distribution of Afropavo in Zaire, which is far removed from the Asian distribution of all other pheasant species. We obtained complete cytochrome b and partial D-loop sequences of Afropavo and compared them to Pavo, guineafowl, Francolinus and other galliform taxa. Our results strongly support a close relationship between Afropavo and Pavo, and we were able to reject alternative phylogenetic hypotheses. Molecular clock estimates of the divergence time place the separation of Afropavo and Pavo in the late Miocene. We also discuss other relatives of Afropavo and Pavo and use this information to propose hypotheses regarding the evolution of ornamentation and sexual dimorphism within this group of pheasants. PMID:9364791

  17. Hypotheses on the functional roles of chaotic transitory dynamics

    NASA Astrophysics Data System (ADS)

    Tsuda, Ichiro

    2009-03-01

    In contrast to the conventional static view of the brain, recent experimental data show that an alternative view is necessary for an appropriate interpretation of its function. Some selected problems concerning the cortical transitory dynamics are discussed. For the first time, we propose five scenarios for the appearance of chaotic itinerancy, which provides typical transitory dynamics. Second, we describe the transitory behaviors that have been observed in human and animal brains. Finally, we propose nine hypotheses on the functional roles of such dynamics, focusing on the dynamics embedded in data and the dynamical interpretation of brain activity within the framework of cerebral hermeneutics.

  18. The Phylogenetic Likelihood Library

    PubMed Central

    Flouri, T.; Izquierdo-Carrasco, F.; Darriba, D.; Aberer, A.J.; Nguyen, L.-T.; Minh, B.Q.; Von Haeseler, A.; Stamatakis, A.

    2015-01-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2–10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). PMID:25358969

  19. Phylogenetically resolving epidemiologic linkage

    PubMed Central

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-01-01

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

  20. Phylogenetically resolving epidemiologic linkage

    DOE PAGESBeta

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-02-22

    The use of phylogenetic trees in epidemiological investigations has become commonplace, but their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the truemore » transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. Moreover, we confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.« less

  1. The phylogenetic likelihood library.

    PubMed

    Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

    2015-03-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). PMID:25358969

  2. Phylogenetically resolving epidemiologic linkage.

    PubMed

    Romero-Severson, Ethan O; Bulla, Ingo; Leitner, Thomas

    2016-03-01

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

  3. Phylogenetic aspects of the complement system.

    PubMed

    Zarkadis, I K; Mastellos, D; Lambris, J D

    2001-01-01

    During evolution two general systems of immunity have emerged: innate or, natural immunity and adaptive (acquired), or specific immunity. The innate system is phylogenetically older and is found in some form in all multicellular organisms, whereas the adaptive system appeared about 450 million years ago and is found in all vertebrates except jawless fish. The complement system in higher vertebrates plays an important role as an effector of both the innate and the acquired immune response, and also participates in various immunoregulatory processes. In lower vertebrates complement is activated by the alternative and lectin pathways and is primarily involved in the opsonization of foreign material. The Agnatha (the most primitive vertebrate species) possess the alternative and lectin pathways while cartilaginous fish are the first species in which the classical pathway appears following the emergence of immunoglobulins. The rest of the poikilothermic species, ranging from teleosts to reptilians, appear to contain a well-developed complement system resembling that of the homeothermic vertebrates. It seems that most of the complement components have appeared after the duplication of primordial genes encoding C3/C4/C5, fB/C2, C1s/C1r/MASP-1/MASP-2, and C6/C7/C8/C9 molecules, in a process that led to the formation of distinct activation pathways. However, unlike homeotherms, several species of poikilotherms (e.g. trout) have recently been shown to possess multiple forms of complement components (C3, factor B) that are structurally and functionally more diverse than those of higher vertebrates. We hypothesize that this remarkable diversity has allowed these animals to expand their innate capacity for immune recognition and response. Recent studies have also indicated the possible presence of complement receptors in protochordates and lower vertebrates. In conclusion, there is considerable evidence suggesting that the complement system is present in the entire lineage of

  4. Pectus excavatum: history, hypotheses and treatment options

    PubMed Central

    Brochhausen, Christoph; Turial, Salmai; Müller, Felix K.P.; Schmitt, Volker H.; Coerdt, Wiltrud; Wihlm, Jean-Marie; Schier, Felix; Kirkpatrick, C. James

    2012-01-01

    Pectus excavatum and pectus carinatum represent the most frequent chest wall deformations. However, the pathogenesis is still poorly understood and research results remain inconsistent. To focus on the recent state of knowledge, we summarize and critically discuss the pathological concepts based on the history of these entities, beginning with the first description in the sixteenth century. Based on the early clinical descriptions, we review and discuss the different pathogenetic hypotheses. To open new perspectives for the potential pathomechanisms, the embryonic and foetal development of the ribs and the sternum is highlighted following the understanding that the origin of these deformities is given by the disruption in the maturation of the parasternal region. In the second, different therapeutical techniques are highlighted and based on the pathogenetic hypotheses and the embryological knowledge potential new biomaterial-based perspectives with interesting insights for tissue engineering-based treatment options are presented. PMID:22394989

  5. Multipolar consensus for phylogenetic trees.

    PubMed

    Bonnard, Cécile; Berry, Vincent; Lartillot, Nicolas

    2006-10-01

    Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html PMID:17060203

  6. The Savannah hypotheses: origin, reception and impact on paleoanthropology.

    PubMed

    Bender, Renato; Tobias, Phillip V; Bender, Nicole

    2012-01-01

    The reconstruction of the human past is a complex task characterized by a high level of interdisciplinarity. How do scientists from different fields reach consensus on crucial aspects of paleoanthropological research? The present paper explores this question through an historical analysis of the origin, development, and reception of the savannah hypotheses (SHs). We show that this model neglected to investigate crucial biological aspects which appeared to be irrelevant in scenarios depicting early hominins evolving in arid or semi-arid open plains. For instance, the exploitation of aquatic food resources and other aspects of hominin interaction with water were largely ignored in classical paleoanthropology. These topics became central to alternative ideas on human evolution known as aquatic hypotheses. Since the aquatic model is commonly regarded as highly controversial, its rejection led to a stigmatization of the whole spectrum of topics around water use in non-human hominoids and hominins. We argue that this bias represents a serious hindrance to a comprehensive reconstruction of the human past. Progress in this field depends on clear differentiation between hypotheses proposed to contextualize early hominin evolution in specific environmental settings and research topics which demand the investigation of all relevant facets of early hominins' interaction with complex landscapes. PMID:23272598

  7. Evaluation of seven hypotheses for metamemory performance in rhesus monkeys

    PubMed Central

    Basile, Benjamin M.; Schroeder, Gabriel R.; Brown, Emily Kathryn; Templer, Victoria L.; Hampton, Robert R.

    2014-01-01

    Knowing the extent to which nonhumans and humans share mechanisms for metacognition will advance our understanding of cognitive evolution and will improve selection of model systems for biomedical research. Some nonhuman species avoid difficult cognitive tests, seek information when ignorant, or otherwise behave in ways consistent with metacognition. There is agreement that some nonhuman animals “succeed” in these metacognitive tasks, but little consensus about the cognitive mechanisms underlying performance. In one paradigm, rhesus monkeys visually searched for hidden food when ignorant of the location of the food, but acted immediately when knowledgeable. This result has been interpreted as evidence that monkeys introspectively monitored their memory to adaptively control information seeking. However, convincing alternative hypotheses have been advanced that might also account for the adaptive pattern of visual searching. We evaluated seven hypotheses using a computerized task in which monkeys chose either to take memory tests immediately or to see the answer again before proceeding to the test. We found no evidence to support the hypotheses of behavioral cue association, rote response learning, expectancy violation, response competition, generalized search strategy, or postural mediation. In contrast, we repeatedly found evidence to support the memory monitoring hypothesis. Monkeys chose to see the answer when memory was poor, either from natural variation or experimental manipulation. We found limited evidence that monkeys also monitored the fluency of memory access. Overall, the evidence indicates that rhesus monkeys can use memory strength as a discriminative cue for information seeking, consistent with introspective monitoring of explicit memory. PMID:25365530

  8. Relaxed Phylogenetics and Dating with Confidence

    PubMed Central

    Ho, Simon Y. W; Phillips, Matthew J

    2006-01-01

    In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution. PMID:16683862

  9. Understanding phylogenetic incongruence: lessons from phyllostomid bats

    PubMed Central

    Dávalos, Liliana M; Cirranello, Andrea L; Geisler, Jonathan H; Simmons, Nancy B

    2012-01-01

    All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive

  10. A Universal Phylogenetic Tree.

    ERIC Educational Resources Information Center

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  11. The Chloroplast Genome of Hyoscyamus niger and a Phylogenetic Study of the Tribe Hyoscyameae (Solanaceae)

    PubMed Central

    Sanchez-Puerta, M. Virginia; Abbona, Cinthia Carolina

    2014-01-01

    The tribe Hyoscyameae (Solanaceae) is restricted to Eurasia and includes the genera Archihyoscyamus, Anisodus, Atropa, Atropanthe, Hyoscyamus, Physochlaina, Przewalskia and Scopolia. Even though the monophyly of Hyoscyameae is strongly supported, the relationships of the taxa within the tribe remain unclear. Chloroplast markers have been widely used to elucidate plant relationships at low taxonomic levels. Identification of variable chloroplast intergenic regions has been developed based on comparative genomics of chloroplast genomes, but these regions have a narrow phylogenetic utility. In this study, we present the chloroplast genome sequence of Hyoscyamus niger and make comparisons to other solanaceous plastid genomes in terms of gene order, gene and intron content, editing sites, origins of replication, repeats, and hypothetical open reading frames. We developed and sequenced three variable plastid markers from eight species to elucidate relationships within the tribe Hyoscyameae. The presence of a horizontally transferred intron in the mitochondrial cox1 gene of some species of the tribe is considered here a likely synapomorphy uniting five genera of the Hyoscyameae. Alternatively, the cox1 intron could be a homoplasious character acquired twice within the tribe. A homoplasious inversion in the intergenic plastid spacer trnC-psbM was recognized as a source of bias and removed from the data set used in the phylogenetic analyses. Almost 12 kb of plastid sequence data were not sufficient to completely resolve relationships among genera of Hyoscyameae but some clades were identified. Two alternative hypotheses of the evolution of the genera within the tribe are proposed. PMID:24851862

  12. Transformation model selection by multiple hypotheses testing

    NASA Astrophysics Data System (ADS)

    Lehmann, Rüdiger

    2014-12-01

    Transformations between different geodetic reference frames are often performed such that first the transformation parameters are determined from control points. If in the first place we do not know which of the numerous transformation models is appropriate then we can set up a multiple hypotheses test. The paper extends the common method of testing transformation parameters for significance, to the case that also constraints for such parameters are tested. This provides more flexibility when setting up such a test. One can formulate a general model with a maximum number of transformation parameters and specialize it by adding constraints to those parameters, which need to be tested. The proper test statistic in a multiple test is shown to be either the extreme normalized or the extreme studentized Lagrange multiplier. They are shown to perform superior to the more intuitive test statistics derived from misclosures. It is shown how model selection by multiple hypotheses testing relates to the use of information criteria like AICc and Mallows' , which are based on an information theoretic approach. Nevertheless, whenever comparable, the results of an exemplary computation almost coincide.

  13. Poisson's ratio over two centuries: challenging hypotheses

    PubMed Central

    Greaves, G. Neville

    2013-01-01

    This article explores Poisson's ratio, starting with the controversy concerning its magnitude and uniqueness in the context of the molecular and continuum hypotheses competing in the development of elasticity theory in the nineteenth century, moving on to its place in the development of materials science and engineering in the twentieth century, and concluding with its recent re-emergence as a universal metric for the mechanical performance of materials on any length scale. During these episodes France lost its scientific pre-eminence as paradigms switched from mathematical to observational, and accurate experiments became the prerequisite for scientific advance. The emergence of the engineering of metals followed, and subsequently the invention of composites—both somewhat separated from the discovery of quantum mechanics and crystallography, and illustrating the bifurcation of technology and science. Nowadays disciplines are reconnecting in the face of new scientific demands. During the past two centuries, though, the shape versus volume concept embedded in Poisson's ratio has remained invariant, but its application has exploded from its origins in describing the elastic response of solids and liquids, into areas such as materials with negative Poisson's ratio, brittleness, glass formation, and a re-evaluation of traditional materials. Moreover, the two contentious hypotheses have been reconciled in their complementarity within the hierarchical structure of materials and through computational modelling. PMID:24687094

  14. Pursuing the method of multiple working hypotheses for hydrological modeling

    NASA Astrophysics Data System (ADS)

    Clark, M. P.; Kavetski, D.; Fenicia, F.

    2012-12-01

    Ambiguities in the representation of environmental processes have manifested themselves in a plethora of hydrological models, differing in almost every aspect of their conceptualization and implementation. The current overabundance of models is symptomatic of an insufficient scientific understanding of environmental dynamics at the catchment scale, which can be attributed to difficulties in measuring and representing the heterogeneity encountered in natural systems. This presentation advocates using the method of multiple working hypotheses for systematic and stringent testing of model alternatives in hydrology. We discuss how the multiple hypothesis approach provides the flexibility to formulate alternative representations (hypotheses) describing both individual processes and the overall system. When combined with incisive diagnostics to scrutinize multiple model representations against observed data, this provides hydrologists with a powerful and systematic approach for model development and improvement. Multiple hypothesis frameworks also support a broader coverage of the model hypothesis space and hence improve the quantification of predictive uncertainty arising from system and component non-identifiabilities. As part of discussing the advantages and limitations of multiple hypothesis frameworks, we critically review major contemporary challenges in hydrological hypothesis-testing, including exploiting different types of data to investigate the fidelity of alternative process representations, accounting for model structure ambiguities arising from major uncertainties in environmental data, quantifying regional differences in dominant hydrological processes, and the grander challenge of understanding the self-organization and optimality principles that may functionally explain and describe the heterogeneities evident in most environmental systems. We assess recent progress in these research directions, and how new advances are possible using multiple hypothesis

  15. Pursuing the method of multiple working hypotheses for hydrological modeling

    NASA Astrophysics Data System (ADS)

    Clark, Martyn P.; Kavetski, Dmitri; Fenicia, Fabrizio

    2011-09-01

    Ambiguities in the representation of environmental processes have manifested themselves in a plethora of hydrological models, differing in almost every aspect of their conceptualization and implementation. The current overabundance of models is symptomatic of an insufficient scientific understanding of environmental dynamics at the catchment scale, which can be attributed to difficulties in measuring and representing the heterogeneity encountered in natural systems. This commentary advocates using the method of multiple working hypotheses for systematic and stringent testing of model alternatives in hydrology. We discuss how the multiple-hypothesis approach provides the flexibility to formulate alternative representations (hypotheses) describing both individual processes and the overall system. When combined with incisive diagnostics to scrutinize multiple model representations against observed data, this provides hydrologists with a powerful and systematic approach for model development and improvement. Multiple-hypothesis frameworks also support a broader coverage of the model hypothesis space and hence improve the quantification of predictive uncertainty arising from system and component nonidentifiabilities. As part of discussing the advantages and limitations of multiple-hypothesis frameworks, we critically review major contemporary challenges in hydrological hypothesis-testing, including exploiting different types of data to investigate the fidelity of alternative process representations, accounting for model structure ambiguities arising from major uncertainties in environmental data, quantifying regional differences in dominant hydrological processes, and the grander challenge of understanding the self-organization and optimality principles that may functionally explain and describe the heterogeneities evident in most environmental systems. We assess recent progress in these research directions, and how new advances are possible using multiple

  16. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study.

    PubMed

    Powell, Alexis F L A; Barker, F Keith; Lanyon, Scott M

    2013-01-01

    Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships. PMID:23000817

  17. Going to the 'Dogs' to Test Hypotheses.

    ERIC Educational Resources Information Center

    Kramm, Kenneth R.

    1982-01-01

    Describes an alternative method for using live animals in the classroom. A toy dog, the "Trail Tracker Hound Dog" (manufactured by CPG Products Corporation, Cincinnati, Ohio), is used to encourage development of such skills as observation, hypothesis testing, and collection and analysis of scientific data. (Author/JN)

  18. Payment for Environmental Services: Hypotheses and Evidence

    PubMed Central

    Alston, Lee J.; Andersson, Krister; Smith, Steven M.

    2014-01-01

    The use of payment for environmental services (PES) is not a new type of contract, but PES programs have become more in vogue because of the potential for sequestering carbon by paying to prevent deforestation and degradation of forestlands. We provide a framework utilizing transaction costs to hypothesize which services are more likely to be provided effectively. We then interpret the literature on PES programs to see the extent to which transaction costs vary as predicted across the type of service and to assess the performance of PES programs. As predicted, we find that transaction costs are the least for club goods like water and greatest for pure public goods like carbon reduction. Actual performance is difficult to measure and varies across the examples. More work and experimentation are needed to gain a better outlook on what elements support effective delivery of environmental services. PMID:25143798

  19. Payment for Environmental Services: Hypotheses and Evidence.

    PubMed

    Alston, Lee J; Andersson, Krister; Smith, Steven M

    2013-06-01

    The use of payment for environmental services (PES) is not a new type of contract, but PES programs have become more in vogue because of the potential for sequestering carbon by paying to prevent deforestation and degradation of forestlands. We provide a framework utilizing transaction costs to hypothesize which services are more likely to be provided effectively. We then interpret the literature on PES programs to see the extent to which transaction costs vary as predicted across the type of service and to assess the performance of PES programs. As predicted, we find that transaction costs are the least for club goods like water and greatest for pure public goods like carbon reduction. Actual performance is difficult to measure and varies across the examples. More work and experimentation are needed to gain a better outlook on what elements support effective delivery of environmental services. PMID:25143798

  20. Recent etiologic hypotheses concerning breast cancer

    SciTech Connect

    Gammon, M.D.; John, E.M. )

    1993-01-01

    A few studies have noted moderate elevation in the risk of breast cancer among women with residential exposure to electromagnetic fields, among women without a history of much strenuous physical activity, and among women with in utero exposures that may indicate high levels of maternal estrogen. The relative risk for each of these associations has generally been less than 2, with little adjustment for possible confounding factors. Also, several studies have not been able to confirm these relations. Currently there is scant or no evidence that silicone breast implants or psychological factors increase the risk of breast cancer. Despite the limited number of studies, the inconsistent results, and the difficulty of measuring several of these exposures, the plausible biologic mechanisms for each indicate that more research on these hypotheses is warranted. 66 refs.

  1. Assessing hypotheses about nesting site occupancy dynamics

    USGS Publications Warehouse

    Bled, Florent; Royle, J. Andrew; Cam, Emmanuelle

    2011-01-01

    Hypotheses about habitat selection developed in the evolutionary ecology framework assume that individuals, under some conditions, select breeding habitat based on expected fitness in different habitat. The relationship between habitat quality and fitness may be reflected by breeding success of individuals, which may in turn be used to assess habitat quality. Habitat quality may also be assessed via local density: if high-quality sites are preferentially used, high density may reflect high-quality habitat. Here we assessed whether site occupancy dynamics vary with site surrogates for habitat quality. We modeled nest site use probability in a seabird subcolony (the Black-legged Kittiwake, Rissa tridactyla) over a 20-year period. We estimated site persistence (an occupied site remains occupied from time t to t + 1) and colonization through two subprocesses: first colonization (site creation at the timescale of the study) and recolonization (a site is colonized again after being deserted). Our model explicitly incorporated site-specific and neighboring breeding success and conspecific density in the neighborhood. Our results provided evidence that reproductively "successful'' sites have a higher persistence probability than "unsuccessful'' ones. Analyses of site fidelity in marked birds and of survival probability showed that high site persistence predominantly reflects site fidelity, not immediate colonization by new owners after emigration or death of previous owners. There is a negative quadratic relationship between local density and persistence probability. First colonization probability decreases with density, whereas recolonization probability is constant. This highlights the importance of distinguishing initial colonization and recolonization to understand site occupancy. All dynamics varied positively with neighboring breeding success. We found evidence of a positive interaction between site-specific and neighboring breeding success. We addressed local

  2. Canonical phylogenetic ordination.

    PubMed

    Giannini, Norberto P

    2003-10-01

    A phylogenetic comparative method is proposed for estimating historical effects on comparative data using the partitions that compose a cladogram, i.e., its monophyletic groups. Two basic matrices, Y and X, are defined in the context of an ordinary linear model. Y contains the comparative data measured over t taxa. X consists of an initial tree matrix that contains all the xj monophyletic groups (each coded separately as a binary indicator variable) of the phylogenetic tree available for those taxa. The method seeks to define the subset of groups, i.e., a reduced tree matrix, that best explains the patterns in Y. This definition is accomplished via regression or canonical ordination (depending on the dimensionality of Y) coupled with Monte Carlo permutations. It is argued here that unrestricted permutations (i.e., under an equiprobable model) are valid for testing this specific kind of groupwise hypothesis. Phylogeny is either partialled out or, more properly, incorporated into the analysis in the form of component variation. Direct extensions allow for testing ecomorphological data controlled by phylogeny in a variation partitioning approach. Currently available statistical techniques make this method applicable under most univariate/multivariate models and metrics; two-way phylogenetic effects can be estimated as well. The simplest case (univariate Y), tested with simulations, yielded acceptable type I error rates. Applications presented include examples from evolutionary ethology, ecology, and ecomorphology. Results showed that the new technique detected previously overlooked variation clearly associated with phylogeny and that many phylogenetic effects on comparative data may occur at particular groups rather than across the entire tree. PMID:14530135

  3. The structure of child and adolescent psychopathology: generating new hypotheses.

    PubMed

    Lahey, Benjamin B; Applegate, Brooks; Waldman, Irwin D; Loft, John D; Hankin, Benjamin L; Rick, Jacqueline

    2004-08-01

    To begin to resolve conflicts among current competing taxonomies of child and adolescent psychopathology, the authors developed an interview covering the symptoms of anxiety, depression, inattention, and disruptive behavior used in the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV; American Psychiatric Association, 1994), the International Statistical Classification of Diseases and Related Health Problems (ICD-10; World Health Organization, 1992), and several implicit taxonomies. This interview will be used in the future to compare the internal and external validity of alternative taxonomies. To provide an informative framework for future hypothesis-testing studies, the authors used principal factor analysis to induce new testable hypotheses regarding the structure of this item pool in a representative sample of 1,358 children and adolescents ranging in age from 4 to 17 years. The resulting hypotheses differed from the DSM-IV, particularly in suggesting that some anxiety symptoms are part of the same syndrome as depression, whereas separation anxiety, fears, and compulsions constitute a separate anxiety dimension. PMID:15311983

  4. Telocytes and Their Extracellular Vesicles-Evidence and Hypotheses.

    PubMed

    Cretoiu, Dragos; Xu, Jiahong; Xiao, Junjie; Cretoiu, Sanda M

    2016-01-01

    Entering the new millennium, nobody believed that there was the possibility of discovering a new cellular type. Nevertheless, telocytes (TCs) were described as a novel kind of interstitial cell. Ubiquitously distributed in the extracellular matrix of any tissue, TCs are regarded as cells with telopodes involved in intercellular communication by direct homo- and heterocellular junctions or by extracellular vesicle (EVs) release. Their discovery has aroused the interest of many research groups worldwide, and many researchers regard them as potentially regenerative cells. Given the experience of our laboratory, where these cells were first described, we review the evidence supporting the fact that TCs release EVs, and discuss alternative hypotheses about their future implications. PMID:27529228

  5. Telocytes and Their Extracellular Vesicles—Evidence and Hypotheses

    PubMed Central

    Cretoiu, Dragos; Xu, Jiahong; Xiao, Junjie; Cretoiu, Sanda M.

    2016-01-01

    Entering the new millennium, nobody believed that there was the possibility of discovering a new cellular type. Nevertheless, telocytes (TCs) were described as a novel kind of interstitial cell. Ubiquitously distributed in the extracellular matrix of any tissue, TCs are regarded as cells with telopodes involved in intercellular communication by direct homo- and heterocellular junctions or by extracellular vesicle (EVs) release. Their discovery has aroused the interest of many research groups worldwide, and many researchers regard them as potentially regenerative cells. Given the experience of our laboratory, where these cells were first described, we review the evidence supporting the fact that TCs release EVs, and discuss alternative hypotheses about their future implications. PMID:27529228

  6. Phylogenetic analyses of a combined data set suggest that the Attheya lineage is the closest living relative of the pennate diatoms (Bacillariophyceae).

    PubMed

    Sorhannus, Ulf; Fox, Martin G

    2012-03-01

    A Bayesian analysis of a seven gene data set was conducted to reconstruct phylogenetic relationships among a sample of centric and pennate diatoms and to test alternative hypotheses about the closest living relative of Bacillariophyceae. A lineage, composed of two Attheya species, was inferred to share the most recent common ancestor with Bacillariophyceae--a relationship that was also corroborated by the combined parsimony analysis. All competing hypotheses about the closest living relative of Bacillariophyceae were rejected because 100% of the trees in the post-burn-in sample in the Bayesian analysis supported the Attheya-Bacillariophyceae clade. According to a partitioned Bremer support analysis, the majority of the genes in the combined data matrix supported the Attheya--Bacillariophyceae relationship. The global topology of the phylogenetic tree indicated that a monophyletic group consisting of Thalassiosirales and Toxarium undulatum formed the deepest branch followed by a node uniting a clade composed of Bacillariophyceae/Attheya species and a lineage made up of Eucampia zoodiacus, Chaetocerotales, Lithodesmiales, Triceratiales, Biddulphiales and Cymatosirales. Except for the phylogenetic positions of Lithodesmiales, Thalassiosira sp and Skeletonema costatum, the optimal tree obtained from the combined parsimony analysis showed the same branching order of taxa as those seen in the consensus tree inferred from three independent Markov chain Monte Carlo analyses. Noteworthy findings are that Toxarium undulatum shares a strongly supported node with Thalassiosirales and that the genus Attheya is not a member of the Chaetocerotales lineage. PMID:21723193

  7. Testable Hypotheses for Unbalanced Neuroimaging Data

    PubMed Central

    McFarquhar, Martyn

    2016-01-01

    Unbalanced group-level models are common in neuroimaging. Typically, data for these models come from factorial experiments. As such, analyses typically take the form of an analysis of variance (ANOVA) within the framework of the general linear model (GLM). Although ANOVA theory is well established for the balanced case, in unbalanced designs there are multiple ways of decomposing the sums-of-squares of the data. This leads to several methods of forming test statistics when the model contains multiple factors and interactions. Although the Type I–III sums of squares have a long history of debate in the statistical literature, there has seemingly been no consideration of this aspect of the GLM in neuroimaging. In this paper we present an exposition of these different forms of hypotheses for the neuroimaging researcher, discussing their derivation as estimable functions of ANOVA models, and discussing the relative merits of each. Finally, we demonstrate how the different hypothesis tests can be implemented using contrasts in analysis software, presenting examples in SPM and FSL. PMID:27378839

  8. Ensemble evaluation of hydrological model hypotheses

    NASA Astrophysics Data System (ADS)

    Krueger, Tobias; Freer, Jim; Quinton, John N.; MacLeod, Christopher J. A.; Bilotta, Gary S.; Brazier, Richard E.; Butler, Patricia; Haygarth, Philip M.

    2010-07-01

    It is demonstrated for the first time how model parameter, structural and data uncertainties can be accounted for explicitly and simultaneously within the Generalized Likelihood Uncertainty Estimation (GLUE) methodology. As an example application, 72 variants of a single soil moisture accounting store are tested as simplified hypotheses of runoff generation at six experimental grassland field-scale lysimeters through model rejection and a novel diagnostic scheme. The fields, designed as replicates, exhibit different hydrological behaviors which yield different model performances. For fields with low initial discharge levels at the beginning of events, the conceptual stores considered reach their limit of applicability. Conversely, one of the fields yielding more discharge than the others, but having larger data gaps, allows for greater flexibility in the choice of model structures. As a model learning exercise, the study points to a "leaking" of the fields not evident from previous field experiments. It is discussed how understanding observational uncertainties and incorporating these into model diagnostics can help appreciate the scale of model structural error.

  9. Phylogenetic Comparative Assembly

    NASA Astrophysics Data System (ADS)

    Husemann, Peter; Stoye, Jens

    Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a contig adjacency graph. From this a layout graph can be computed which indicates putative adjacencies of the contigs in order to aid biologists in finishing the complete genomic sequence.

  10. Bayesian phylogenetic estimation of fossil ages.

    PubMed

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  11. Bayesian phylogenetic estimation of fossil ages

    PubMed Central

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  12. Electroconvulsive Treatment: Hypotheses about Mechanisms of Action

    PubMed Central

    Fosse, Roar; Read, John

    2013-01-01

    No consensus has been reached on the mode of action of electroconvulsive treatment (ECT). We suggest that two features may aid in the delineation of the involved mechanisms. First, when effective, ECT would be likely to affect brain functions that are typically altered in its primary recipient group, people with severe depression. Central among these are the frontal and temporal lobes, the hypothalamus-pituitary-adrenal (HPA) stress axis, and the mesocorticolimbic dopamine system. Second, the involved mechanisms should be affected for a time period that matches the average endurance of clinical effects, which is indicated to be several days to a few weeks. To identify effects upon frontal and temporal lobe functioning we reviewed human studies using EEG, PET, SPECT, and fMRI. Effects upon the HPA axis and the dopamine system were assessed by reviewing both human and animal studies. The EEG studies indicate that ECT decelerates neural activity in the frontal and temporal lobes (increased delta and theta wave activity) for weeks to months. Comparable findings are reported from PET and SPECT studies, with reduced cerebral blood flow (functional deactivation) for weeks to months after treatment. The EEG deceleration and functional deactivation following ECT are statistically associated with reduced depression scores. FMRI studies indicate that ECT flattens the pattern of activation and deactivation that is associated with cognitive task performance and alters cortical functional connectivity in the ultra slow frequency range. A common finding from human and animal studies is that ECT acutely activates both the HPA axis and the dopamine system. In considering this evidence, we hypothesize that ECT affects the brain in a similar manner as severe stress or brain trauma which activates the HPA axis and the dopamine system and may compromise frontotemporal functions. PMID:23986724

  13. Entanglement, Invariants, and Phylogenetics

    NASA Astrophysics Data System (ADS)

    Sumner, J. G.

    2007-10-01

    This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics and its analysis is a relatively new technique where most progress to date has been achieved by using discrete mathematics. This thesis takes a group theoretical approach to the problem by beginning with a remarkable mathematical parallel to the process of scattering in particle physics. This is shown to equate to branching events in the evolutionary history of molecular units. The major technical result of this thesis is the derivation of existence proofs and computational techniques for calculating polynomial group invariant functions on a multi-linear space where the group action is that relevant to a Markovian time evolution. The practical results of this thesis are an extended analysis of the use of invariant functions in distance based methods and the presentation of a new reconstruction technique for quartet trees which is consistent with the most general Markov model of sequence evolution.

  14. Phylogenetic trees in bioinformatics

    SciTech Connect

    Burr, Tom L

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  15. Evolutionary relationships of the Critically Endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses

    PubMed Central

    2014-01-01

    Background The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many instances. The phylogenetic relationships of the Ethiopian endemic monotypic genus Ericabatrachus has been addressed thus far only with phenotypic data and remains contentious. Results We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes. Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a close relationship with cacosternines or Phrynobatrachus. Conclusions We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa. Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies. PMID:24612655

  16. Phylogenetic Diversification of the Globin Gene Superfamily in Chordates

    PubMed Central

    Storz, Jay F.; Opazo, Juan C.; Hoffmann, Federico G.

    2015-01-01

    Summary Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this paper is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do this we present a consensus phylogeny of the chordate globin gene superfamily. We document the relative roles of gene duplication and whole-genome duplication in fueling the functional diversification of vertebrate globins, and we unravel patterns of shared ancestry among globin genes from representatives of the three chordate subphyla (Craniata, Urochordata, and Cephalochordata). Our results demonstrate the value of integrating phylogenetic analyses with genomic analyses of conserved synteny to infer the duplicative origins and evolutionary histories of globin genes. We also discuss a number of case studies that illustrate the importance of phylogenetic information when making inferences about the evolution of globin gene expression and protein function. Finally, we discuss why the globin gene superfamily presents special challenges for phylogenetic analysis, and we describe methodological approaches that can be used to meet those challenges. PMID:21557448

  17. The Phylogenetic Diversity of Metagenomes

    PubMed Central

    Kembel, Steven W.; Eisen, Jonathan A.; Pollard, Katherine S.; Green, Jessica L.

    2011-01-01

    Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context. PMID:21912589

  18. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

    PubMed Central

    2011-01-01

    Background Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies. Results We found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca) as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus) within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris) from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis) as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic. Conclusion Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the resolution of a strongly

  19. Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

    PubMed

    Barr, W Andrew; Scott, Robert S

    2014-04-01

    In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, <5.6% of DFAs and <8.26% of PGLS analyses were significant. When characters contained phylogenetic signal and actual habitats were used, 33.27 to 45.07% of DFAs and <13.09% of PGLS analyses were significant. False Discovery Rate (FDR) corrections for multiple PGLS analyses reduced the rate of significance to <4.64%. In all cases using actual habitats and characters with phylogenetic signal, correct classification rates of DFAs exceeded random chance. In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was. In short, DFA offered no indication that differences between categories might be explained by phylogenetic signal, while PGLS did. As such, PGLS provides a valuable tool for testing the functional hypotheses at the heart of ecomorphology. PMID:24382658

  20. Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

    PubMed

    Wang, Ning; Braun, Edward L; Kimball, Rebecca T

    2012-02-01

    Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA-DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses. Although different alignments and analyses yielded slightly different results, our analyses excluded all but one of the five a priori hypotheses. In many cases, the passerines were sister to the Psittaciformes (parrots), and taxa were members of a larger clade that includes Falconidae (falcons) and Cariamidae (seriemas). However, the position of Coliiformes (mousebirds) was highly unstable in our analyses of 30 loci, and this represented the primary source of incongruence among analyses. Mousebirds were united with passerines or parrots in some analyses

  1. Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

    PubMed Central

    Dees, Jonathan; Niemi, Jarad; Montplaisir, Lisa

    2014-01-01

    Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. PMID:25452489

  2. About hypotheses and paradigms: exploring the Discreetness-Chance Paradigm.

    PubMed

    Kaellis, Eugene

    2006-01-01

    Hypotheses generally conform to paradigms which, over time, change, usually tardily, after they have become increasingly difficult to sustain under the impact of non-conforming evidence and alternative hypotheses, but more important, when they no longer are comfortably ensconced in the surrounding social-economic-political-cultural milieu. It is asserted that this milieu is the most important factor in shaping scientific theorizing. Some examples are cited: the rejection of the evidence that the world orbits around the sun (suspected by Pythagoras) in favor of centuries-long firm adherence to the Ptolemaic geocentric system; the early acceptance of Natural Selection in spite of its tautological essence and only conjectural supporting evidence, because it justified contemporaneous social-political ideologies as typified by, e.g., Spencer and Malthus. Economic, social, and cultural factors are cited as providing the ground, i.e., ideational substrate, for what is cited as the Discreetness-Chance Paradigm (DCP), that has increasingly dominated physics, biology, and medicine for over a century and which invokes small, discrete packets of energy/matter (quanta, genes, microorganisms, aberrant cells) functioning within an environment of statistical, not determined, causality. There is speculation on a possible paradigmatic shift from the DCP, which has fostered the proliferation, parallel with ("splitting") taxonomy, of alleged individual disease entities, their diagnoses, and, when available, their specific remedies, something particularly prominent in, e.g., psychiatry's Diagnostic and Statistical Manual, a codified compendium of alleged mental and behavioral disorders, but evident in any textbook of diagnosis and treatment of physical ailments. This presumed paradigm shift may be reflected in Western medicine, presently increasingly empirical and atomized, towards a growing acceptance of a more generalized, subject-oriented, approach to health and disease, a non

  3. Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses

    PubMed Central

    Morgan-Richards, Mary; Hills, Simon F. K.; Biggs, Patrick J.; Trewick, Steven A.

    2016-01-01

    Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii) with its putative paternal diploid taxon (Clitarchus hookeri), a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity of the hybrid daughter genome. The scale of genome sequencing required was conveniently achieved by extracting mRNA and sequencing cDNA to examine expressed allelic diversity. This allowed us to test hybrid-progenitor relationships among non-model organisms with large genomes and different ploidy levels. Examination of thousands of independent loci avoids potential problems produced by the silencing of parts of one or other of the parental genomes, a phenomenon sometimes associated with the process of stabilisation of a hybrid genome. Transcript assembles were assessed for evidence of paralogs and/or alternative splice variants before proceeding. Comparison of transcript assemblies was not an appropriate measure of genetic variability, but by mapping reads back to clusters derived from each species we determined levels of allelic diversity. We found greater cDNA sequence diversity among alleles in the putative hybrid species (Acanthoxyla geisovii) than the non-hybrid. The allelic diversity within the putative paternal species (Clitachus hookeri) nested within the hybrid-daughter genome, supports the current view of a hybrid-progenitor relationship for these stick insect species. Next generation sequencing technology provides opportunities for testing evolutionary hypotheses with non-model organisms, including, as here, genomes that are large due to polyploidy. PMID:27187689

  4. How Journalists Describe Their Stories: Hypotheses and Assumptions in Newsmaking.

    ERIC Educational Resources Information Center

    Stocking, S. Holly; LaMarca, Nancy

    1990-01-01

    Interviews newspaper reporters to show that journalists, like scientists, usually have hypotheses in mind in working a story. Finds, however, that unlike those of scientists, journalists' hypotheses were both explicit and implicit. (MG)

  5. Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest

    PubMed Central

    Staggemeier, Vanessa Graziele; Diniz-Filho, José Alexandre Felizola; Forest, Félix; Lucas, Eve

    2015-01-01

    Background and Aims Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade. Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas. Key Results Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot. Conclusions This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside

  6. Sequence Data, Phylogenetic Inference, and Implications of Downward Causation.

    PubMed

    Fitzhugh, Kirk

    2016-06-01

    Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain 'morphological' characters but selection cannot be causally applied to sequences since fitness differences cannot be directly associated with individual nucleotides or amino acids. The relation of selection to sequence data is by way of downward or top-down causation from those phenotypes upon which selection occurs. The application of phylogenetic inference to explain sequence data is thus restricted to instances where drift is the relevant theory; those nucleotides or amino acids that can be explained via downward causation are precluded from inclusion in the data matrix. The restrictions on the inclusion of sequence data in phylogenetic inferences equally apply to species hypotheses, precluding the more restrictive approach known as DNA barcoding. Not being able to discern drift and selection as relevant causal mechanisms can severely constrain the inclusion and explanations of sequence data. Implications of such exclusion are discussed in relation to the requirement of total evidence. PMID:26961079

  7. Phylogenetic analysis reveals a scattered distribution of autumn colours

    PubMed Central

    Archetti, Marco

    2009-01-01

    Background and Aims Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved. Methods Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves. Key Results Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times. Conclusions The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection. PMID:19126636

  8. Quartets and unrooted phylogenetic networks.

    PubMed

    Gambette, Philippe; Berry, Vincent; Paul, Christophe

    2012-08-01

    Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions. PMID:22809417

  9. Phylogenetics and the Human Microbiome

    PubMed Central

    Matsen, Frederick A.

    2015-01-01

    The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work. PMID:25102857

  10. Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)

    PubMed Central

    López-Arbarello, Adriana

    2012-01-01

    The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic

  11. [Phylogenetic relationships among schistosomatidae].

    PubMed

    Beer, S A; Voronin, M V; Zazornova, O P; Khrisanfova, G G; Semenova, S K

    2010-01-01

    According updates on molecular genetics, the development of human schistosomes in Asia with subsequent migration to the African continent is considered to be the most probable course of events. Generally, there are 2 hypotheses of the genus Schistoma. A hypothesis of Gondvana origin was based on snail host phylogeny and paleonthology and considered first schistosomes to originate on this continent to and appear in Asia from the Indian subcontinent platform 70-150 million years ago and in South America before Gondvana's split 60-120 million years ago. The recent data of molecular genetics show a high similarity between ITS2 sequences of S.bovis and S.intercalatum, with slightly lesser one between S.bovis and S.matthei. The similar pattern with slightly fewer differences can be seen in variability of cytochrome C subunit 1. Webster et al. 2006 noted a generally high similarity among species of the African group of schistosomes and considered it to originate from interspecies hybridization inside this group. Such hydridization occurring in both nature and a laboratory can make uncertain the determination of schistosome species based on a certain single gene marker. PMID:20608188

  12. Complex phylogenetic distribution of a non-canonical genetic code in green algae

    PubMed Central

    2010-01-01

    Background A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and non-canonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code. Results This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique. Conclusions We compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikely because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate model, whereby the non-canonical code observed in these green algal orders has a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have been completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was not followed by final

  13. Head size, weaponry, and cervical adaptation: Testing craniocervical evolutionary hypotheses in Ceratopsia.

    PubMed

    VanBuren, Collin S; Campione, Nicolás E; Evans, David C

    2015-07-01

    The anterior cervical vertebrae form the skeletal connection between the cranial and postcranial skeletons in higher tetrapods. As a result, the morphology of the atlas-axis complex is likely to be shaped by selection pressures acting on either the head or neck. The neoceratopsian (Reptilia:Dinosauria) syncervical represents one of the most highly modified atlas-axis regions in vertebrates, being formed by the complete coalescence of the three most anterior cervical vertebrae. In ceratopsids, the syncervical has been hypothesized to be an adaptation to support a massive skull, or to act as a buttress during intraspecific head-to-head combat. Here, we test these functional/adaptive hypotheses within a phylogenetic framework and critically examine the previously proposed methods for quantifying relative head size in the fossil record for the first time. Results indicate that neither the evolution of cranial weaponry nor large head size correlates with the origin of cervical fusion in ceratopsians, and we, therefore, reject both adaptive hypotheses for the origin of the syncervical. Anterior cervical fusion has evolved independently in a number of amniote clades, and further research on extant groups with this peculiar anatomy is needed to understand the evolutionary basis for cervical fusion in Neoceratopsia. PMID:26095296

  14. Phylogenetic lineages in Pseudocercospora

    PubMed Central

    Crous, P.W.; Braun, U.; Hunter, G.C.; Wingfield, M.J.; Verkley, G.J.M.; Shin, H.-D.; Nakashima, C.; Groenewald, J.Z.

    2013-01-01

    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general

  15. Phylogenetic review of tonal sound production in whales in relation to sociality

    PubMed Central

    May-Collado, Laura J; Agnarsson, Ingi; Wartzok, Douglas

    2007-01-01

    Background It is widely held that in toothed whales, high frequency tonal sounds called 'whistles' evolved in association with 'sociality' because in delphinids they are used in a social context. Recently, whistles were hypothesized to be an evolutionary innovation of social dolphins (the 'dolphin hypothesis'). However, both 'whistles' and 'sociality' are broad concepts each representing a conglomerate of characters. Many non-delphinids, whether solitary or social, produce tonal sounds that share most of the acoustic characteristics of delphinid whistles. Furthermore, hypotheses of character correlation are best tested in a phylogenetic context, which has hitherto not been done. Here we summarize data from over 300 studies on cetacean tonal sounds and social structure and phylogenetically test existing hypotheses on their co-evolution. Results Whistles are 'complex' tonal sounds of toothed whales that demark a more inclusive clade than the social dolphins. Whistles are also used by some riverine species that live in simple societies, and have been lost twice within the social delphinoids, all observations that are inconsistent with the dolphin hypothesis as stated. However, cetacean tonal sounds and sociality are intertwined: (1) increased tonal sound modulation significantly correlates with group size and social structure; (2) changes in tonal sound complexity are significantly concentrated on social branches. Also, duration and minimum frequency correlate as do group size and mean minimum frequency. Conclusion Studying the evolutionary correlation of broad concepts, rather than that of their component characters, is fraught with difficulty, while limits of available data restrict the detail in which component character correlations can be analyzed in this case. Our results support the hypothesis that sociality influences the evolution of tonal sound complexity. The level of social and whistle complexity are correlated, suggesting that complex tonal sounds play an

  16. Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies.

    PubMed

    Fortunato, Laura; Jordan, Fiona

    2010-12-12

    Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship 'facts'. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families. PMID:21041215

  17. Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA.

    PubMed

    Waits, L P; Sullivan, J; O'Brien, S J; Ward, R H

    1999-10-01

    The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species. PMID:10508542

  18. Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies

    PubMed Central

    Fortunato, Laura; Jordan, Fiona

    2010-01-01

    Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship ‘facts’. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families. PMID:21041215

  19. Two issues in archaeological phylogenetics: taxon construction and outgroup selection.

    PubMed

    O'Brien, Michael J; Lyman, R Lee; Saab, Youssef; Saab, Elias; Darwent, John; Glover, Daniel S

    2002-03-21

    Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup. PMID:12051970

  20. Phylogenetic Approaches Toward Crocodylian History

    NASA Astrophysics Data System (ADS)

    Brochu, Christopher A.

    A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record without consideration of phylogenetic relationships. The three main extant crocodylian lineagesGavialoidea, Alligatoroidea, Crocodyloideaare known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions that are best explained by the crossing of marine barriers during the Tertiary. Early Tertiary crocodylian faunas are phylogenetically composite, and clades tend to be morphologically uniform and geographically widespread. Later in the Tertiary, Old World crocodylian faunas are more endemic. Crocodylian phylogeneticists face numerous challenges, the most important being the phylogenetic relationships and time of divergence of the two living gharials (Gavialis gangeticus and Tomistoma schlegelii), the relationships among living true crocodiles (Crocodylus), and the relationships among caimans.

  1. [Phylogenetic analysis of Pleurotus species].

    PubMed

    Shnyreva, A A; Shnyreva, A V

    2015-02-01

    We performed phylogenetic analysis for ten Pleurotus species, based on internal transcribed spacer (ITS) sequences of rDNA. A phylogenetic tree was constructed on the basis of 31 oyster fungi strains of different origin and 10 reference sequences from GenBank. Our analysis demonstrates that the tested Pleurotus species are of monophyletic origin. We evaluated the evolutionary distances between these species. Classic genetic analysis of sexual compatibility based on monocaryon (mon)-mon crosses showed no reproductive barriers within the P. cornucopiae-P. euosmus species complex. Thus, despite the divergence (subclustering) between commercial strains and natural isolates of P. ostreatus revealed by phylogenetic analysis, there is no reproductive isolation between these groups. A common allele of the matB locus was identified for the commercial strains Sommer and L/4, supporting the common origin of these strains. PMID:25966583

  2. A survey of etiologic hypotheses among testicular cancer researchers

    PubMed Central

    Stang, Andreas; Trabert, Britton; Rusner, Carsten; Poole, Charles; Almstrup, Kristian; Meyts, Ewa Rajpert-De; McGlynn, Katherine A.

    2015-01-01

    Basic research results can provide new ideas and hypotheses to be examined in epidemiological studies. We conducted a survey among testicular cancer researchers on hypotheses concerning the etiology of this malignancy. All researchers on the mailing list of Copenhagen Testis Cancer Workshops and corresponding authors of PubMed-indexed articles identified by the search term “testicular cancer” and published within 10 years (in total 2750 recipients) were invited to respond to an e-mail based survey. Participants of the 8th Copenhagen Testis Cancer Workshop in May 2014 were subsequently asked to rate the plausibility of the suggested etiologic hypotheses on a scale of 1 (very implausible) to 10 (very plausible). This report describes the methodology of the survey, the score distributions by individual hypotheses, hypothesis group and the participants’ major research fields, and discuss the hypotheses that scored as most plausible. We also present plans for improving the survey that may be repeated at a next international meeting of experts in testicular cancer. Overall 52 out of 99 (53%) registered participants of the 8th Copenhagen Testis Cancer Workshop submitted the plausibility rating form. Fourteen out of 27 hypotheses were related to exposures during pregnancy. Hypotheses with the highest mean plausibility ratings were either related to prenatal exposures or exposures that might have an effect during pregnancy and in post-natal life. The results of the survey may be helpful for triggering more specific etiologic hypotheses that include factors related to endocrine disruption, DNA damage, inflammation, and nutrition during pregnancy. The survey results may stimulate a multidisciplinary discussion about new etiologic hypotheses of testicular cancer. PMID:25538016

  3. High-resolution phylogenetic microbial community profiling.

    PubMed

    Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; Bowman, Brett; Bowers, Robert M; Levy, Asaf; Gies, Esther A; Cheng, Jan-Fang; Copeland, Alex; Klenk, Hans-Peter; Hallam, Steven J; Hugenholtz, Philip; Tringe, Susannah G; Woyke, Tanja

    2016-08-01

    Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential. PMID:26859772

  4. Interpreting the universal phylogenetic tree

    PubMed Central

    Woese, Carl R.

    2000-01-01

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist. PMID:10900003

  5. Interpreting the universal phylogenetic tree

    NASA Technical Reports Server (NTRS)

    Woese, C. R.

    2000-01-01

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

  6. Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes).

    PubMed

    Golombek, Anja; Tobergte, Sarah; Struck, Torsten H

    2015-05-01

    Gnathostomulida is a taxon of small marine worms, which exclusively inhabit the interstitium. The evolution of Gnathostomulida has been discussed for decades. Originally regarded as primitive animals with affinities to flatworms, the phylogenetic position of Gnathostomulida has been debated. Given the lack of an anus a close relationship to Platyhelminthes has been maintained (i.e., Plathelminthomorpha hypothesis). Alternative hypotheses proposed Gnathostomulida as being close to Gastrotricha due to the presence of a monociliary epidermis (i.e., Monokonta/Neotrichozoa hypothesis) or to Syndermata based on the complicated jaw apparatus (i.e., Gnathifera hypothesis). Molecular analyses using only few genes were inconclusive. Recent phylogenomic studies brought some progress by placing Gnathostomulida as sister to Syndermata, but support for this relationship was low and depended on the analytical strategy. Herein we present the first data of complete or nearly complete mitochondrial genomes for two gnathostomulids (Gnathostomula paradoxa &G. armata), one gastrotrich (Lepidodermella squamata) and one polyclad flatworm (Stylochoplana maculata) to address the uncertain phylogenetic affinity of Gnathostomulida. Our analyses found Gnathostomulida as sister to Syndermata (Gnathifera hypothesis). Thorough sensitivity analyses addressing taxon instability, branch length heterogeneity (also known as long branch attraction) and base composition heterogeneity showed that the position of Gnathostomulida is consistent across the different analyses and, hence, independent of potential misleading biases. Moreover, by ameliorating these different biases nodal support values could be increased to maximum values. Thus, our data support the hypothesis that the different jaw apparatuses of Syndermata and Gnathostomulida are indeed homologous structures as proposed by the Gnathifera hypothesis. PMID:25796325

  7. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data.

    PubMed

    Fernandes, Noemi M; Paiva, Thiago da Silva; da Silva-Neto, Inácio D; Schlegel, Martin; Schrago, Carlos G

    2016-02-01

    Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree. PMID:26549427

  8. Test of Alternative Hypotheses Explaining the Comorbidity between Attention-Deficit/Hyperactivity Disorder and Conduct Disorder

    ERIC Educational Resources Information Center

    Rhee, Soo Hyun; Willcutt, Erik G.; Hartman, Christie A.; Pennington, Bruce F.; DeFries, John C.

    2008-01-01

    There is significant comorbidity between attention-deficit/hyperactivity disorder (ADHD) and conduct disorder (CD). The conclusions of studies that examined the causes of comorbidity between ADHD and CD conflict, with some researchers finding support for the three independent disorders model and others finding support for the correlated risk…

  9. Does Ease to Block a Ball Affect Perceived Ball Speed? Examination of Alternative Hypotheses

    ERIC Educational Resources Information Center

    Witt, Jessica K.; Sugovic, Mila

    2012-01-01

    According to an action-specific account of perception, the perceived speed of a ball can be a function of the ease to block the ball. Balls that are easier to stop look like they are moving slower than balls that are more difficult to stop. This was recently demonstrated with a modified version of the classic computer game Pong (Witt & Sugovic,…

  10. Phylogenetic Relationships Among Lepidium Papilliferum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous phylogenetic analyses of Lepidium included only a few acessions of L. montanum, L. flavum, and L. fremontii to represent western North Amrican species. Two additional species endemic to southwest Idaho have posed both taxonomic and conservation questions regarding their species status. Le...

  11. Information search in the testing of quantified hypotheses: how "all," "most," "some," "few," and "none" hypotheses are tested.

    PubMed

    Sanbonmatsu, David M; Posavac, Steven S; Vanous, Sam; Ho, Edward A

    2005-02-01

    A series of experiments examined how the search for information in the testing of hypotheses is affected by quantifiers that specify the frequency of the test relation. The experiments showed that a positive search is used more in the testing of propositions in which some instances are predicted to have the test relation than in the testing of propositions in which most or few instances are predicted to have the test relation. In addition, the studies demonstrated that a negative or disconfirmatory search is more likely to characterize tests of absolute hypotheses than tests of hypotheses of the majority or minority form. Finally, the findings indicated that a negative search also is more common in tests of hypotheses predicting the absence rather than the presence of a phenomenon. Thus, as expected, participants generally engaged in a diagnostic search rather than the confirmatory search for information that has been so ubiquitous in previous research. PMID:15619597

  12. HyQue: evaluating hypotheses using Semantic Web technologies

    PubMed Central

    2011-01-01

    Background Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. Results We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. Conclusions HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. PMID:21624158

  13. Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

    PubMed

    Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

    2015-10-01

    Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species. PMID:26649382

  14. Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian collision: A molecular phylogenetic perspective and an area cladogram for Central Asia.

    PubMed

    Macey, J R; Wang, Y; Ananjeva, N B; Larson, A; Papenfuss, T J

    1999-08-01

    A well-supported phylogenetic hypothesis is presented for gekkonid lizards of the genus Teratoscincus. Phylogenetic relationships of four of the five species are investigated using 1733 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase). A single most parsimonious tree depicts T. przewalskii and T. roborowskii as a monophyletic group, with T. scincus as their sister taxon and T. microlepis as the sister taxon to the clade containing the first three species. The aligned sequences contain 341 phylogenetically informative characters. Each node is supported by a bootstrap value of 100% and the shortest suboptimal tree requires 29 additional steps. Allozymic variation is presented for proteins encoded by 19 loci but these data are largely uninformative phylogenetically. Teratoscincus species occur on tectonic plates of Gondwanan origin that were compressed by the impinging Indian Subcontinent, resulting in massive montane uplifting along plate boundaries. Taxa occurring in China (Tarim Block) form a monophyletic group showing vicariant separation from taxa in former Soviet Central Asia and northern Afghanistan (Farah Block); alternative biogeographic hypotheses are statistically rejected. This vicariant event involved the rise of the Tien Shan-Pamir and is well dated to 10 million years before present. Using this date for separation of taxa occurring on opposite sides of the Tien Shan-Pamir, an evolutionary rate of 0.57% divergence per lineage per million years is calculated. This rate is similar to estimates derived from fish, bufonid frogs, and agamid lizards for the same region of the mitochondrial genome ( approximately 0.65% divergence per lineage per million years). Evolutionary divergence of the mitochondrial genome has a surprisingly stable rate across vertebrates. PMID

  15. Delinquency and Peer Acceptance in Adolescence: A Within-Person Test of Moffitt’s Hypotheses

    PubMed Central

    Rulison, Kelly L; Kreager, Derek A.; Osgood, D. Wayne

    2015-01-01

    We tested two hypotheses derived from Moffitt’s (1993) taxonomic theory of antisocial behavior, both of which are central to her explanation for the rise in delinquency during adolescence. Specifically, we tested whether persistently delinquent individuals become more accepted by their peers during adolescence and whether individuals who abstain from delinquent behavior become less accepted. Participants were 4,359 adolescents from 14 communities in the PROSPER study, which assessed friendship networks and delinquency from 6th (M = 11.8 years) to 9th (M = 15.3 years) grade. We operationalized peer acceptance as: number of nominations received (indegree centrality), attractiveness as a friend (adjusted indegree centrality), and network bridging potential (betweenness centrality) and tested the hypotheses using multilevel modeling. Contrary to Moffitt’s hypothesis, persistently delinquent youth did not become more accepted between early and middle adolescence, and although abstainers were less accepted in early adolescence, they became more accepted over time. Results were similar for boys and girls; when differences occurred, they provided no support for Moffitt’s hypotheses for boys and were opposite of her hypotheses for girls. Sensitivity analyses using alternative strategies and additional data to identify persistently delinquent adolescents produced similar results. We explore the implications of these results for Moffitt’s assertions that social mimicry of persistently antisocial adolescents leads to increases in delinquency and that social isolation leads to abstention. PMID:25243328

  16. Delinquency and peer acceptance in adolescence: a within-person test of Moffitt's hypotheses.

    PubMed

    Rulison, Kelly L; Kreager, Derek A; Osgood, D Wayne

    2014-11-01

    We tested 2 hypotheses derived from Moffitt's (1993) taxonomic theory of antisocial behavior, both of which are central to her explanation for the rise in delinquency during adolescence. We tested whether persistently delinquent individuals become more accepted by their peers during adolescence and whether individuals who abstain from delinquent behavior become less accepted. Participants were 4,359 adolescents from 14 communities in the PROSPER study, which assessed friendship networks and delinquency from 6th (M = 11.8 years) to 9th (M = 15.3 years) grade. We operationalized peer acceptance as number of nominations received (indegree centrality), attractiveness as a friend (adjusted indegree centrality), and network bridging potential (betweenness centrality) and tested the hypotheses with multilevel modeling. Contrary to Moffitt's hypothesis, persistently delinquent youths did not become more accepted between early and middle adolescence, and although abstainers were less accepted in early adolescence, they became more accepted over time. Results were similar for boys and girls; when differences occurred, they provided no support for Moffitt's hypotheses for boys and were opposite of her hypotheses for girls. Sensitivity analyses in which alternative strategies and additional data were used to identify persistently delinquent adolescents produced similar results. We explore the implications of these results for Moffitt's assertions that social mimicry of persistently antisocial adolescents leads to increases in delinquency and that social isolation leads to abstention. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PMID:25243328

  17. Testing species-level diversification hypotheses in Madagascar: the case of microendemic Brookesia leaf chameleons.

    PubMed

    Townsend, Ted M; Vieites, David R; Glaw, Frank; Vences, Miguel

    2009-12-01

    Madagascar's flora and fauna are remarkable both for their diversity and supraspecific endemism. Moreover, many taxa contain large numbers of species with limited distributions. Several hypotheses have been proposed to explain this high level of microendemism, including 1) riverine barrier, 2) mountain refuge, and 3) watershed contraction hypotheses, the latter 2 of which center on fragmentation due to climatic shifts associated with Pliocene/Pleistocene glaciations. The Malagasy leaf chameleon genus Brookesia is a speciose group with a high proportion of microendemic taxa, thus making it an excellent candidate to test these vicariance scenarios. We used mitochondrial and nuclear sequence data to construct a Brookesia phylogeny, and temporal concordance with Pliocene/Pleistocene speciation scenarios was tested by estimating divergence dates using a relaxed-clock Bayesian method. We strongly reject a role for Pliocene/Pleistocene climatic fluctuations in species-level diversification of Brookesia. We also used simulations to test the spatial predictions of the watershed contraction model in a phylogenetic context, independent of its temporal component, and found no statistical support for this model. The riverine barrier model is likewise a qualitatively poor fit to our data, but some relationships support a more ancient mountain refuge effect. We assessed support for the 3 hypotheses in a nonphylogenetic context by examining altitude and species richness and found a significant positive correlation between these variables. This is consistent with a mountain refuge effect but does not support the watershed contraction or riverine barrier models. Finally, we find repeated higher level east-west divergence patterns 1) between the 2 sister clades comprising the Brookesia minima group and 2) within the clade of larger leaf chameleons, which shows a basal divergence between western and eastern/northern sister clades. Our results highlight the central role of phylogeny in

  18. Morphometric study of phylogenetic and ecologic signals in procyonid (mammalia: carnivora) endocasts.

    PubMed

    Ahrens, Heather E

    2014-12-01

    Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology. PMID:25066912

  19. Generating penetration path hypotheses for decision support in multiple trauma.

    PubMed Central

    Ogunyemi, O.; Kaye, J.; Webber, B.; Clarke, J. R.

    1995-01-01

    We present a 3D graphical system that allows users to visualize different penetration path hypotheses for (multiple) gunshot or stab wounds, using a 3D graphical model of a human body with appropriate anatomical structures. The system also identifies the anatomical structures associated with each hypothesis. The various penetration path hypotheses follow from a combinatorial analysis of the set of surface wounds. The affected structures are determined by performing a detailed interpenetration analysis between 3D models of a penetration path and each anatomical structure within the body. Images Figure 2 Figure 3 PMID:8563315

  20. Phylogenetic analysis of otospiralin protein

    PubMed Central

    Torktaz, Ibrahim; Behjati, Mohaddeseh; Rostami, Amin

    2016-01-01

    Background: Fibrocyte-specific protein, otospiralin, is a small protein, widely expressed in the central nervous system as neuronal cell bodies and glia. The increased expression of otospiralin in reactive astrocytes implicates its role in signaling pathways and reparative mechanisms subsequent to injury. Indeed, otospiralin is considered to be essential for the survival of fibrocytes of the mesenchymal nonsensory regions of the cochlea. It seems that other functions of this protein are not yet completely understood. Materials and Methods: Amino acid sequences of otospiralin from 12 vertebrates were derived from National Center for Biotechnology Information database. Phylogenetic analysis and phylogeny estimation were performed using MEGA 5.0.5 program, and neighbor-joining tree was constructed by this software. Results: In this computational study, the phylogenetic tree of otospiralin has been investigated. Therefore, dendrograms of otospiralin were depicted. Alignment performed in MUSCLE method by UPGMB algorithm. Also, entropy plot determined for a better illustration of amino acid variations in this protein. Conclusion: In the present study, we used otospiralin sequence of 12 different species and by constructing phylogenetic tree, we suggested out group for some related species. PMID:27099854

  1. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction.

    PubMed

    Fernández, Rosa; Edgecombe, Gregory D; Giribet, Gonzalo

    2016-09-01

    Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal

  2. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

    PubMed Central

    Fernández, Rosa; Edgecombe, Gregory D.; Giribet, Gonzalo

    2016-01-01

    Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal

  3. The life cycle of Phaeocystis (Prymnesiophycaea): evidence and hypotheses

    NASA Astrophysics Data System (ADS)

    Rousseau, V.; Vaulot, D.; Casotti, R.; Cariou, V.; Lenz, J.; Gunkel, J.; Baumann, M.

    1994-04-01

    The present paper reviews the literature related to the life cycle of the prymnesiophyte Phaeocystis and its controlling factors and proposes novel hypotheses based on unpublished observations in culture and in the field. We chiefly refer to P. globosa Scherffel as most of the observations concern this species. P. globosa exhibits a complex alternation between several types of free-living cells (non-motile, flagellates, microzoopores and possibly macrozoospores) and colonies for which neither forms nor pathways have been completely identified and described. The different types of Phaeocystis cells were reappraised on the basis of existing microscopic descriptions complemented by unpublished flow cytometric investigations. This analysis revealed the existence of at least three different types of free-living cells identified on the basis of a combination of size, motility and ploidy characteristics: non-motile cells, flagellates and microzoospores. Their respective function within Phaeocystis life cycle, and in particular their involvement in colony formation is not completely understood. Observational evidence shows that Phaeocystis colonies are initiated at the early stage of their bloom each by one free-living cell. The mechanisms controlling this cellular transformation are still uncertain due to the lack of information on the overwintering Phaeocystis fomms and on the cell type responsible for colony induction. The existence of haploid microzoospores released from senescent colonies gives however some support to sexuality involvement at some stages of colony formation. Once colonies are formed, at least two mechanisms were identified as responsible of the spreading of colony form: colony multiplication by colonial division or budding and induction of new colony from colonial cells released in the external medium after colony disruption. The latter mechanism was clearly identified, involving at least two successive cell differentiations in the following sequence

  4. Organizational Culture and Effectiveness in Higher Education: A Test of the "Culture Type" and "Strong Culture" Hypotheses.

    ERIC Educational Resources Information Center

    Smart, John C.; St. John, Edward P.

    1996-01-01

    The relative merits of two prominent lines of inquiry into the linkage between organizational culture and effectiveness (culture type and strong culture hypotheses) were studied with 334 colleges and universities. Findings support both approaches and suggest that alternative culture types are differentially effective on different performance…

  5. Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps.

    PubMed

    Eickhoff, Simon B; Heim, Stefan; Zilles, Karl; Amunts, Katrin

    2006-08-15

    The statistical inference on functional imaging data is severely complicated by the embedded multiple testing problem. Defining a region of interest (ROI) where the activation is hypothesized a priori helps to circumvent this problem, since in this case the inference is restricted to fewer simultaneous tests, rendering it more sensitive. Cytoarchitectonic maps obtained from postmortem brains provide objective, a priori ROIs that can be used to test anatomically specified hypotheses about the localization of functional activations. We here analyzed three methods for the definition of ROIs based on probabilistic cytoarchitectonic maps. (1) ROIs defined by the volume assigned to a cytoarchitectonic area in the summary map of all areas (maximum probability map, MPM), (2) ROIs based on thresholding the individual probabilistic maps and (3) spherical ROIs build around the cytoarchitectonic center of gravity. The quality with which the thus defined ROIs represented the respective cytoarchitectonic areas as well as their sensitivity for detecting functional activations was subsequently statistically evaluated. Our data showed that the MPM method yields ROIs, which reflect most adequately the underlying anatomical hypotheses. These maps also show a high degree of sensitivity in the statistical analysis. We thus propose the use of MPMs for the definition of ROIs. In combination with thresholding based on the Gaussian random field theory, these ROIs can then be applied to test anatomically specified hypotheses in functional neuroimaging studies. PMID:16781166

  6. Landscape moderation of biodiversity patterns and processes - eight hypotheses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding how landscape characteristics affect local biodiversity patterns and ecological processes is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest the following seven hypotheses, which we hope w...

  7. Modelling Analysis of Students' Processes of Generating Scientific Explanatory Hypotheses

    ERIC Educational Resources Information Center

    Park, Jongwon

    2006-01-01

    It has recently been determined that generating an explanatory hypothesis to explain a discrepant event is important for students' conceptual change. The purpose of this study is to investigate how students' generate new explanatory hypotheses. To achieve this goal, questions are used to identify students prior ideas related to electromagnetic…

  8. Bayes Factor Approaches for Testing Interval Null Hypotheses

    ERIC Educational Resources Information Center

    Morey, Richard D.; Rouder, Jeffrey N.

    2011-01-01

    Psychological theories are statements of constraint. The role of hypothesis testing in psychology is to test whether specific theoretical constraints hold in data. Bayesian statistics is well suited to the task of finding supporting evidence for constraint, because it allows for comparing evidence for 2 hypotheses against each another. One issue…

  9. Toward Valid Measurement of Stephen Pepper's World Hypotheses.

    ERIC Educational Resources Information Center

    Johnson, John A.

    Two measures of the "world hypotheses" of Stephen Pepper were mailed to 100 sociobiologists, 87 behaviorists, 79 personality psychologists, and 45 human developmentalists. The World Hypothesis Scale (WHS) was designed to measure Pepper's four world views: (1) formism; (2) mechanism; (3) organicism; and (4) contextualism. The Organicism-Mechanism…

  10. Addressing Moderated Mediation Hypotheses: Theory, Methods, and Prescriptions

    ERIC Educational Resources Information Center

    Preacher, Kristopher J.; Rucker, Derek D.; Hayes, Andrew F.

    2007-01-01

    This article provides researchers with a guide to properly construe and conduct analyses of conditional indirect effects, commonly known as moderated mediation effects. We disentangle conflicting definitions of moderated mediation and describe approaches for estimating and testing a variety of hypotheses involving conditional indirect effects. We…

  11. Cohort Variation in Happiness: Some Hypotheses and Exploratory Analyses.

    ERIC Educational Resources Information Center

    Felton, Barbara J.

    1987-01-01

    Drew portraits of two cohorts of older adults from historical and sociological sources and tested hypotheses about cohort-specific values with data collected in 1957 and 1976. Results support view that adults born before 1900 were distinctive from other cohorts in that their happiness levels were closely linked with survival needs and firmly…

  12. Detection of horizontal gene transfers from phylogenetic comparisons.

    PubMed

    Pylro, Victor Satler; Vespoli, Luciano de Souza; Duarte, Gabriela Frois; Yotoko, Karla Suemy Clemente

    2012-01-01

    Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases. PMID:22675653

  13. Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation.

    PubMed

    Letsch, Harald O; Greve, Carola; Kück, Patrick; Fleck, Günther; Stocsits, Roman R; Misof, Bernhard

    2009-12-01

    Secondary structure models of mitochondrial and nuclear (r)RNA sequences are frequently applied to aid the alignment of these molecules in phylogenetic analyses. Additionally, it is often speculated that structure variation of (r)RNA sequences might profitably be used as phylogenetic markers. The benefit of these approaches depends on the reliability of structure models. We used a recently developed approach to show that reliable inference of large (r)RNA secondary structures as a prerequisite of simultaneous sequence and structure alignment is feasible. The approach iteratively establishes local structure constraints of each sequence and infers fully folded individual structures by constrained MFE optimization. A comparison of structure edit distances of individual constraints and fully folded structures showed pronounced phylogenetic signal in fully folded structures. As model sequences we characterized secondary structures of 28S rRNA sequences of selected insects and examined their phylogenetic signal according to established phylogenetic hypotheses. PMID:19654047

  14. Causes of bat fatalities at wind turbines: Hypotheses and predictions

    USGS Publications Warehouse

    Cryan, P.M.; Barclay, R.M.R.

    2009-01-01

    Thousands of industrial-scale wind turbines are being built across the world each year to meet the growing demand for sustainable energy. Bats of certain species are dying at wind turbines in unprecedented numbers. Species of bats consistently affected by turbines tend to be those that rely on trees as roosts and most migrate long distances. Although considerable progress has been made in recent years toward better understanding the problem, the causes of bat fatalities at turbines remain unclear. In this synthesis, we review hypothesized causes of bat fatalities at turbines. Hypotheses of cause fall into 2 general categoriesproximate and ultimate. Proximate causes explain the direct means by which bats die at turbines and include collision with towers and rotating blades, and barotrauma. Ultimate causes explain why bats come close to turbines and include 3 general types: random collisions, coincidental collisions, and collisions that result from attraction of bats to turbines. The random collision hypothesis posits that interactions between bats and turbines are random events and that fatalities are representative of the bats present at a site. Coincidental hypotheses posit that certain aspects of bat distribution or behavior put them at risk of collision and include aggregation during migration and seasonal increases in flight activity associated with feeding or mating. A surprising number of attraction hypotheses suggest that bats might be attracted to turbines out of curiosity, misperception, or as potential feeding, roosting, flocking, and mating opportunities. Identifying, prioritizing, and testing hypothesized causes of bat collisions with wind turbines are vital steps toward developing practical solutions to the problem. ?? 2009 American Society of Mammalogists.

  15. Transforming phylogenetic networks: Moving beyond tree space.

    PubMed

    Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

    2016-09-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. PMID:27224010

  16. Phylogenetic placement of the Spirosomaceae

    NASA Technical Reports Server (NTRS)

    Woese, C. R.; Maloy, S.; Mandelco, L.; Raj, H. D.

    1990-01-01

    Comparative analysis of 16S rRNA sequences shows that the family Spirosomaceae belongs within the eubacterial phylum defined by the flavobacteria and bacteriodes. Its constituent genera, Spirosoma, Flectobacillus, and Runella form a monophyletic grouping therein. The phylogenetic assignment is based not only upon evolutionary distance analysis, but also upon sequence signatures and higher order structural synapomorphies in 16S rRNA. Another genus peripherally associated with the Spirosomaceae, Ancylobacter ("Microcyclus"), does not cluster with the flavobacteria and their relatives, but rather belongs to the alpha subdivision of the purple bacteria.

  17. Phylogenetic Analysis of Poliovirus Sequences.

    PubMed

    Jorba, Jaume

    2016-01-01

    Comparative genomic sequencing is a major surveillance tool in the Polio Laboratory Network. Due to the rapid evolution of polioviruses (~1 % per year), pathways of virus transmission can be reconstructed from the pathways of genomic evolution. Here, we describe three main phylogenetic methods; estimation of genetic distances, reconstruction of a maximum-likelihood (ML) tree, and estimation of substitution rates using Bayesian Markov chain Monte Carlo (MCMC). The data set used consists of complete capsid sequences from a survey of poliovirus sequences available in GenBank. PMID:26983737

  18. Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities

    PubMed Central

    Hardoim, Cristiane C. P.; Esteves, Ana I. S.; Pires, Francisco R.; Gonçalves, Jorge M. S.; Cox, Cymon J.; Xavier, Joana R.; Costa, Rodrigo

    2012-01-01

    Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family - Sarcotragus spinosulus and Ircinia variabilis – in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of S. spinosulus and I. variabilis differed markedly from each other – with higher number of ribotypes observed in S. spinosulus – and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria). Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria), respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis. These

  19. Phylogenetic analysis and trait evolution in Australian lineages of drywood termites (Isoptera, Kalotermitidae).

    PubMed

    Thompson, G J; Miller, L R; Lenz, M; Crozier, R H

    2000-12-01

    A phylogenetic analysis of Australian drywood termites (Isoptera, Kalotermitidae) based on partial sequence from the cytochrome oxidase II (COII) and cytochrome b genes is presented. In addition to providing new information on the evolutionary relationships among 25 species from seven genera, we evaluate the relative likelihoods of alternative topological hypotheses, including those derived from morphology-based classifications. We also test the applicability of a molecular clock for estimating the age of the Kalotermitidae and infer the evolution of species-specific variation for habitat type and soldier caste phragmosis by mapping this information onto the independently derived phylogeny. Maximum-likelihood analysis of both nucleotide and protein sequences from a multigene data set jointly support a single topology, which is shown to be the best estimate of the true phylogeny among the alternatives tested. Our results support the monophyly of all genera but question the discrimination between Procryptotermes and Cryptotermes. A basal dichotomy among generic groups suggests two principle lines of divergence within the family. Intergeneric relationships show mixed congruence to previous proposals, resulting in one morphology-based classification being rejected. A molecular clock hypothesis is not supported due to significant among-lineage rate heterogeneity in the COII gene. Patterns revealed through trait mapping suggest that the most recently diverged taxa tend to occupy the driest habitats and that these same taxa reflect a defensive transition away from large mandibulate soldiers toward small phragmotic soldiers. The association between habitat and defensibility supports the hypothesis that these two characters have been tightly linked throughout the social diversification of termites. PMID:11133196

  20. Generalized Sequential Probability Ratio Test for Separate Families of Hypotheses

    PubMed Central

    Li, Xiaoou; Liu, Jingchen; Ying, Zhiliang

    2014-01-01

    In this paper, we consider the problem of testing two separate families of hypotheses via a generalization of the sequential probability ratio test. In particular, the generalized likelihood ratio statistic is considered and the stopping rule is the first boundary crossing of the generalized likelihood ratio statistic. We show that this sequential test is asymptotically optimal in the sense that it achieves asymptotically the shortest expected sample size as the maximal type I and type II error probabilities tend to zero.

  1. An experimentally determined evolutionary model dramatically improves phylogenetic fit.

    PubMed

    Bloom, Jesse D

    2014-08-01

    All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses. PMID:24859245

  2. Phylogenetic Origins of Brain Organisers

    PubMed Central

    Robertshaw, Ellen; Kiecker, Clemens

    2012-01-01

    The regionalisation of the nervous system begins early in embryogenesis, concomitant with the establishment of the anteroposterior (AP) and dorsoventral (DV) body axes. The molecular mechanisms that drive axis induction appear to be conserved throughout the animal kingdom and may be phylogenetically older than the emergence of bilateral symmetry. As a result of this process, groups of patterning genes that are equally well conserved are expressed at specific AP and DV coordinates of the embryo. In the emerging nervous system of vertebrate embryos, this initial pattern is refined by local signalling centres, secondary organisers, that regulate patterning, proliferation, and axonal pathfinding in adjacent neuroepithelium. The main secondary organisers for the AP neuraxis are the midbrain-hindbrain boundary, zona limitans intrathalamica, and anterior neural ridge and for the DV neuraxis the notochord, floor plate, and roof plate. A search for homologous secondary organisers in nonvertebrate lineages has led to controversy over their phylogenetic origins. Based on a recent study in hemichordates, it has been suggested that the AP secondary organisers evolved at the base of the deuterostome superphylum, earlier than previously thought. According to this view, the lack of signalling centres in some deuterostome lineages is likely to reflect a secondary loss due to adaptive processes. We propose that the relative evolutionary flexibility of secondary organisers has contributed to a broader morphological complexity of nervous systems in different clades. PMID:24278699

  3. Phylogenetic Conservatism in Plant Phenology

    NASA Technical Reports Server (NTRS)

    Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

    2013-01-01

    Phenological events defined points in the life cycle of a plant or animal have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism the tendency for closely related species to share similar ecological and biological attributes in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing 4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses.Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories.

  4. Phylogeny and Classification of the Trapdoor Spider Genus Myrmekiaphila: An Integrative Approach to Evaluating Taxonomic Hypotheses

    PubMed Central

    Bailey, Ashley L.; Brewer, Michael S.; Hendrixson, Brent E.; Bond, Jason E.

    2010-01-01

    Background Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. Methods and Findings Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. Conclusions Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of “Dollo evolution” wherein a complex character evolves only once

  5. Lifelong Socio Economic Position and biomarkers of later life health: testing the contribution of competing hypotheses.

    PubMed

    Ploubidis, George B; Benova, Lenka; Grundy, Emily; Laydon, Daniel; DeStavola, Bianca

    2014-10-01

    The relative contribution of early or later life Socio Economic Position (SEP) to later life health is not fully understood and there are alternative hypotheses about the pathways through which they may influence health. We used data from the English Longitudinal Study of Ageing with a formal approach for the identification of mediating factors in order to investigate alternative hypotheses about life course influences on biomarkers of later life health. We found that early life SEP predicts physical health at least 65 years later. However, a more complicated pattern of associations than that implied by previous findings was also observed. Age group specific effects emerged, with current SEP dominating the effect on later life physical health and fibrinogen levels in participants under 65, while early life SEP had a more prominent role in explaining inequalities in physical health for men and women over 75. We extend previous findings on mid adulthood and early old age, to old age and the beginnings of late old age. The complexity of our findings highlights the need for further research on the mechanisms that underlie the association between SEP and later life health. PMID:24636422

  6. Phylogenetic analysis of the spirochetes.

    PubMed Central

    Paster, B J; Dewhirst, F E; Weisburg, W G; Tordoff, L A; Fraser, G J; Hespell, R B; Stanton, T B; Zablen, L; Mandelco, L; Woese, C R

    1991-01-01

    The 16S rRNA sequences were determined for species of Spirochaeta, Treponema, Borrelia, Leptospira, Leptonema, and Serpula, using a modified Sanger method of direct RNA sequencing. Analysis of aligned 16S rRNA sequences indicated that the spirochetes form a coherent taxon composed of six major clusters or groups. The first group, termed the treponemes, was divided into two subgroups. The first treponeme subgroup consisted of Treponema pallidum, Treponema phagedenis, Treponema denticola, a thermophilic spirochete strain, and two species of Spirochaeta, Spirochaeta zuelzerae and Spirochaeta stenostrepta, with an average interspecies similarity of 89.9%. The second treponeme subgroup contained Treponema bryantii, Treponema pectinovorum, Treponema saccharophilum, Treponema succinifaciens, and rumen strain CA, with an average interspecies similarity of 86.2%. The average interspecies similarity between the two treponeme subgroups was 84.2%. The division of the treponemes into two subgroups was verified by single-base signature analysis. The second spirochete group contained Spirochaeta aurantia, Spirochaeta halophila, Spirochaeta bajacaliforniensis, Spirochaeta litoralis, and Spirochaeta isovalerica, with an average similarity of 87.4%. The Spirochaeta group was related to the treponeme group, with an average similarity of 81.9%. The third spirochete group contained borrelias, including Borrelia burgdorferi, Borrelia anserina, Borrelia hermsii, and a rabbit tick strain. The borrelias formed a tight phylogenetic cluster, with average similarity of 97%. THe borrelia group shared a common branch with the Spirochaeta group and was closer to this group than to the treponemes. A single spirochete strain isolated fromt the shew constituted the fourth group. The fifth group was composed of strains of Serpula (Treponema) hyodysenteriae and Serpula (Treponema) innocens. The two species of this group were closely related, with a similarity of greater than 99%. Leptonema illini

  7. Ant Abundance along a Productivity Gradient: Addressing Two Conflicting Hypotheses

    PubMed Central

    Segev, Udi; Kigel, Jaime; Lubin, Yael; Tielbörger, Katja

    2015-01-01

    The number of individuals within a population or community and their body size can be associated with changes in resource supply. While these relationships may provide a key to better understand the role of abiotic vs. biotic constraints in animal communities, little is known about the way size and abundance of organisms change along resource gradients. Here, we studied this interplay in ants, addressing two hypotheses with opposite predictions regarding variation in population densities along resource gradients- the ‘productivity hypothesis’ and the ‘productivity-based thinning hypothesis’. The hypotheses were tested in two functional groups of ground-dwelling ants that are directly primary consumers feeding on seeds: specialized seed-eaters and generalist species. We examined variations in colony density and foraging activity (a size measurement of the forager caste) in six ant assemblages along a steep productivity gradient in a semi-arid region, where precipitation and plant biomass vary 6-fold over a distance of 250km. An increase in the density or foraging activity of ant colonies along productivity gradients is also likely to affect competitive interactions among colonies, and consequently clinal changes in competition intensity were also examined. Ant foraging activity increased with productivity for both functional groups. However, colony density revealed opposing patterns: it increased with productivity for the specialized seed-eaters, but decreased for the generalist species. Competition intensity, evaluated by spatial partitioning of species at food baits and distribution of colonies, was uncorrelated with productivity in the specialized seed-eaters, but decreased with increasing productivity in the generalists. Our results provide support for two contrasting hypotheses regarding the effect of resource availability on the abundance of colonial organisms- the ‘productivity hypothesis’ for specialized seed-eaters and the

  8. Conceptual Modeling of mRNA Decay Provokes New Hypotheses

    PubMed Central

    Somekh, Judith; Haimovich, Gal; Guterman, Adi; Dori, Dov; Choder, Mordechai

    2014-01-01

    Biologists are required to integrate large amounts of data to construct a working model of the system under investigation. This model is often informal and stored mentally or textually, making it prone to contain undetected inconsistencies, inaccuracies, or even contradictions, not much less than a representation in free natural language. Using Object-Process Methodology (OPM), a formal yet visual and humanly accessible conceptual modeling language, we have created an executable working model of the mRNA decay process in Saccharomyces cerevisiae, as well as the import of its components to the nucleus following mRNA decay. We show how our model, which incorporates knowledge from 43 articles, can reproduce outcomes that match the experimental findings, evaluate hypotheses, and predict new possible outcomes. Moreover, we were able to analyze the effects of the mRNA decay model perturbations related to gene and interaction deletions, and predict the nuclear import of certain decay factors, which we then verified experimentally. In particular, we verified experimentally the hypothesis that Rpb4p, Lsm1p, and Pan2p remain bound to the RNA 3′-untralslated region during the entire process of the 5′ to 3′ degradation of the RNA open reading frame. The model has also highlighted erroneous hypotheses that indeed were not in line with the experimental outcomes. Beyond the scientific value of these specific findings, this work demonstrates the value of the conceptual model as an in silico vehicle for hypotheses generation and testing, which can reinforce, and often even replace, risky, costlier wet lab experiments. PMID:25255440

  9. Ant Abundance along a Productivity Gradient: Addressing Two Conflicting Hypotheses.

    PubMed

    Segev, Udi; Kigel, Jaime; Lubin, Yael; Tielbörger, Katja

    2015-01-01

    The number of individuals within a population or community and their body size can be associated with changes in resource supply. While these relationships may provide a key to better understand the role of abiotic vs. biotic constraints in animal communities, little is known about the way size and abundance of organisms change along resource gradients. Here, we studied this interplay in ants, addressing two hypotheses with opposite predictions regarding variation in population densities along resource gradients- the 'productivity hypothesis' and the 'productivity-based thinning hypothesis'. The hypotheses were tested in two functional groups of ground-dwelling ants that are directly primary consumers feeding on seeds: specialized seed-eaters and generalist species. We examined variations in colony density and foraging activity (a size measurement of the forager caste) in six ant assemblages along a steep productivity gradient in a semi-arid region, where precipitation and plant biomass vary 6-fold over a distance of 250km. An increase in the density or foraging activity of ant colonies along productivity gradients is also likely to affect competitive interactions among colonies, and consequently clinal changes in competition intensity were also examined. Ant foraging activity increased with productivity for both functional groups. However, colony density revealed opposing patterns: it increased with productivity for the specialized seed-eaters, but decreased for the generalist species. Competition intensity, evaluated by spatial partitioning of species at food baits and distribution of colonies, was uncorrelated with productivity in the specialized seed-eaters, but decreased with increasing productivity in the generalists. Our results provide support for two contrasting hypotheses regarding the effect of resource availability on the abundance of colonial organisms- the 'productivity hypothesis' for specialized seed-eaters and the 'productivity-based thinning

  10. The use of extremal hypotheses as a means of predicting alluvial channel dimensions for river restoration

    NASA Astrophysics Data System (ADS)

    Tranmer, A.; Goodwin, P.

    2013-12-01

    In designing fluvial infrastructure and restoration projects the question often arises, what are the cross sectional characteristics of width, depth, roughness, and slope necessary to ensure no net aggradation or degradation occurs within a given reach of river? Current fluvial design utilizes empirical and numerical methods to calculate the required slope and geometry of alluvial channels; however, no solution has been proposed that fully incorporates the necessary 3-dimensional mechanics of open channels due to the complicated processes and feedbacks that occur during mobile bed conditions. This is further compounded by numerous local geologic constraints and perturbations that must be considered, which interrupt the evolution towards a balance of deposition and erosion, or the condition of dynamic-equilibrium. However, given the moderate success of power law relations, such as regime theory and hydraulic geometry, it is evident self-organizing processes are present in watersheds that scale channel size and sinuosity to some average condition in order to maintain a balance of fluid and sediment flux from the upstream catchment. Extremal hypotheses have been developed as an alternative to solving the reach scale 3-dimensional conservation laws for fluid and sediment, to provide a first order means of predicting channel dimensions in an objective and reproducible manner. This study evaluates the performance of extremal hypotheses in identifying the trend towards dynamic-equilibrium over unique spatial gradients in 2 gravel-bed river systems. Using a location-for-time-substitution approach, extremal hypotheses were examined over a longitudinal gradient of channel evolution towards reaches found to be near equilibrium in an unconfined, transport-limited river in the undisturbed rain forest of Chilean Patagonia and a supply-limited, semi-confined canyon system in Central Idaho, USA. Field data from these two sites imply alluvial systems attempt to minimize their

  11. Conceptual change, crucial experiments and auxiliary hypotheses. A theoretical contribution.

    PubMed

    Levinas, Marcelo Leonardo; Carretero, Mario

    2010-12-01

    Theories about conceptual change have been generally related to historical and philosophical analysis of science. Yet, there is still much debate on how ideas coming from the history of science and their implications can be applied in this field. Our study intends to investigate the complex structure of conceptual change, by making use of some particularly representative features of the History and Philosophy of science, while considering the structure of so-called crucial experiments and the specific role of implicit hypotheses. Due to their historical importance and logical reasoning aspects, examining these issues may contribute to understand how conceptual change may take place. PMID:20676827

  12. Generalized procedures for testing hypotheses about survival or recovery rates

    USGS Publications Warehouse

    Sauer, J.R.; Williams, B.K.

    1989-01-01

    Comparisons of survival or recovery rates from different time periods or geographic regions may be difficult to accomplish using the Z-tests suggested by Brownie et al. (1985). We propose a general Chi-square statistic that addresses an unambiguous null hypothesis of homogeneity among several survival or recovery rates. With this statistic, specific hypotheses of differences in rates can be simultaneously tested using contrasts. If necessary, a posteriori multiple comparisons can also be conducted that incorporate an adjustment for Type I error.

  13. Pathogenesis of Bacterial Vaginosis: Discussion of Current Hypotheses.

    PubMed

    Muzny, Christina A; Schwebke, Jane R

    2016-08-15

    In April 2015, the Division of Microbiology and Infectious Diseases of the National Institute of Allergy and Infectious Diseases hosted an experts technical consultation on bacterial vaginosis (BV), where data regarding controversies over the pathogenesis of BV were discussed. The discussion on the epidemiology and pathogenesis of BV is presented here, and several hypotheses on its pathogenesis are critiqued. Rigorous hypothesis-driven studies are needed to ultimately determine the cause of BV. This information is vital for the prevention and control of this important infection and its adverse public health consequences. PMID:27449868

  14. [Hypotheses for the genesis of cancer: a historical perspective].

    PubMed

    Morange, Michel

    2014-01-01

    The explanation of cancer has always been tightly related to the state of knowledge in biology, and its transformations. The present situation is not different. New techniques, such as deep sequencing, are rapidly moving our vision of cancer in an impredictable way. Systems biology, epigenetics, and the study of stem cells are generating new hypotheses on cancer and its evolution. New roles for aleatory events in the genesis of cancer have been proposed. In the traditional opposition between holism and reductionism, organisms and molecules, an intermediary level, the cancer cell, seems to be the most appropriate to study oncogenesis. PMID:25014461

  15. Vaccines and autism: a tale of shifting hypotheses.

    PubMed

    Gerber, Jeffrey S; Offit, Paul A

    2009-02-15

    Although child vaccination rates remain high, some parental concern persists that vaccines might cause autism. Three specific hypotheses have been proposed: (1) the combination measles-mumps-rubella vaccine causes autism by damaging the intestinal lining, which allows the entrance of encephalopathic proteins; (2) thimerosal, an ethylmercury-containing preservative in some vaccines, is toxic to the central nervous system; and (3) the simultaneous administration of multiple vaccines overwhelms or weakens the immune system. We will discuss the genesis of each of these theories and review the relevant epidemiological evidence. PMID:19128068

  16. Phylogenetic organization of bacterial activity

    PubMed Central

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-01-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with 13C and 18O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  17. Phylogenetic organization of bacterial activity.

    PubMed

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-09-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  18. Alternative security

    SciTech Connect

    Weston, B.H. )

    1990-01-01

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview.

  19. Phylogenetic Reconstruction as a Broadly Applicable Teaching Tool in the Biology Classroom: The Value of Data in Estimating Likely Answers

    ERIC Educational Resources Information Center

    Julius, Matthew L.; Schoenfuss, Heiko L.

    2006-01-01

    This laboratory exercise introduces students to a fundamental tool in evolutionary biology--phylogenetic inference. Students are required to create a data set via observation and through mining preexisting data sets. These student data sets are then used to develop and compare competing hypotheses of vertebrate phylogeny. The exercise uses readily…

  20. Phylogenetic analysis of Attalea (Arecaceae): insights on the historical biogeography of a recently diversified Neotropical plant group

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technical Abstract Here we present a dated phylogenetic tree of the neotropical palm genus Attalea (Arecaceae). We used six orthologs from the nuclear WRKY gene family across 98 accessions to address relationships among species and biogeographic hypotheses. Here we found that the formerly recognized...

  1. Action-related auditory ERP attenuation: Paradigms and hypotheses.

    PubMed

    Horváth, János

    2015-11-11

    A number studies have shown that the auditory N1 event-related potential (ERP) is attenuated when elicited by self-induced or self-generated sounds. Because N1 is a correlate of auditory feature- and event-detection, it was generally assumed that N1-attenuation reflected the cancellation of auditory re-afference, enabled by the internal forward modeling of the predictable sensory consequences of the given action. Focusing on paradigms utilizing non-speech actions, the present review summarizes recent progress on action-related auditory attenuation. Following a critical analysis of the most widely used, contingent paradigm, two further hypotheses on the possible causes of action-related auditory ERP attenuation are presented. The attention hypotheses suggest that auditory ERP attenuation is brought about by a temporary division of attention between the action and the auditory stimulation. The pre-activation hypothesis suggests that the attenuation is caused by the activation of a sensory template during the initiation of the action, which interferes with the incoming stimulation. Although each hypothesis can account for a number of findings, none of them can accommodate the whole spectrum of results. It is suggested that a better understanding of auditory ERP attenuation phenomena could be achieved by systematic investigations of the types of actions, the degree of action-effect contingency, and the temporal characteristics of action-effect contingency representation-buildup and -deactivation. This article is part of a Special Issue entitled SI: Prediction and Attention. PMID:25843932

  2. Multiple Hypotheses Testing Procedures in Clinical Trials and Genomic Studies

    PubMed Central

    Pan, Qing

    2013-01-01

    We review and compare multiple hypothesis testing procedures used in clinical trials and those in genomic studies. Clinical trials often employ global tests, which draw an overall conclusion for all the hypotheses, such as SUM test, Two-Step test, Approximate Likelihood Ratio test (ALRT), Intersection-Union Test (IUT), and MAX test. The SUM and Two-Step tests are most powerful under homogeneous treatment effects, while the ALRT and MAX test are robust in cases with non-homogeneous treatment effects. Furthermore, the ALRT is robust to unequal sample sizes in testing different hypotheses. In genomic studies, stepwise procedures are used to draw marker-specific conclusions and control family wise error rate (FWER) or false discovery rate (FDR). FDR refers to the percent of false positives among all significant results and is preferred over FWER in screening high-dimensional genomic markers due to its interpretability. In cases where correlations between test statistics cannot be ignored, Westfall-Young resampling method generates the joint distribution of P-values under the null and maintains their correlation structure. Finally, the GWAS data from a clinical trial searching for SNPs associated with nephropathy among Type 1 diabetic patients are used to illustrate various procedures. PMID:24350232

  3. Hypothesizing dopaminergic genetic antecedents in schizophrenia and substance seeking behavior.

    PubMed

    Blum, Kenneth; Oscar-Berman, Marlene; Badgaiyan, Rajendra D; Palomo, Tomas; Gold, Mark S

    2014-05-01

    The dopamine system has been implicated in both substance use disorder (SUD) and schizophrenia. A recent meta-analysis suggests that A1 allele of the DRD2 gene imposes genetic risk for SUD, especially alcoholism and has been implicated in Reward Deficiency Syndrome (RDS). We hypothesize that dopamine D2 receptor (DRD2) gene Taq1 A2 allele is associated with a subtype of non-SUD schizophrenics and as such may act as a putative protective agent against the development of addiction to alcohol or other drugs of abuse. Schizophrenics with SUD may be carriers of the DRD2 Taq1 A1 allele, and/or other RDS reward polymorphisms and have hypodopaminergic reward function. One plausible mechanism for alcohol seeking in schizophrenics with SUD, based on previous research, may be a deficiency of gamma type endorphins that has been linked to schizophrenic type psychosis. We also propose that alcohol seeking behavior in schizophrenics, may serve as a physiological self-healing process linked to the increased function of the gamma endorphins, thereby reducing abnormal dopaminergic activity at the nucleus accumbens (NAc). These hypotheses warrant further investigation and cautious interpretation. We, therefore, encourage research involving neuroimaging, genome wide association studies (GWAS), and epigenetic investigation into the relationship between neurogenetics and systems biology to unravel the role of dopamine in psychiatric illness and SUD. PMID:24636783

  4. Hypothesizing Dopaminergic Genetic Antecedents in Schizophrenia and Substance Seeking Behavior

    PubMed Central

    Blum, Kenneth; Oscar-Berman, Marlene; Badgaiyan, Rajendra; Palomo, Tomas; Gold, Mark S.

    2014-01-01

    The dopamine system has been implicated in both substance use disorder (SUD) and schizophrenia. A recent meta- analysis suggests that A1 allele of the DRD2 gene imposes genetic risk for SUD, especially alcoholism and has been implicated in Reward Deficiency Syndrome (RDS). We hypothesize that dopamine D2 receptor (DRD2) gene Taq1 A2 allele is associated with a subtype of non- SUD schizophrenics and as such may act as a putative protective agent against the development of addiction to alcohol or other drugs of abuse. Schizophrenics with SUD may be carriers of the DRD2 Taq1 A1 allele, and/or other RDS reward polymorphisms and have hypodopaminergic reward function. One plausible mechanism for alcohol seeking in schizophrenics with SUD, based on previous research, may be a deficiency of gamma type endorphins that has been linked to schizophrenic type psychosis.. We also propose that alcohol seeking behavior in schizophrenics, may serve as a physiological self-healing process linked to the increased function of the gamma endorphins, thereby reducing abnormal dopaminergic activity at the nucleus accumbens (NAc). These hypotheses warrant further investigation and cautious interpretation. We, therefore, encourage research involving neuroimaging, genome wide association studies (GWAS), and epigenetic investigation into the relationship between neurogenetics and systems biology to unravel the role of dopamine in psychiatric illness and SUD. PMID:24636783

  5. Serial Learning in Rats: A Test of Three Hypotheses

    ERIC Educational Resources Information Center

    Capaldi, E. J.; Miller, Ronald Mellado

    2004-01-01

    Findings obtained by providing rats with a single fixed series of events, A-B-C-..., often are equally compatible with three alternative serial learning interpretations: that the signal for items is (A) their position in the series (position view), (B) the prior item of the series (chaining view), and (C) one, two, or more prior items of the…

  6. Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona).

    PubMed

    Zardoya, R; Meyer, A

    2000-06-01

    The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNA(Cys)). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets-one combining protein-coding genes and the other combining tRNA genes-strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated. PMID:10835397

  7. Evolutionary origins of human handedness: evaluating contrasting hypotheses.

    PubMed

    Cochet, Hélène; Byrne, Richard W

    2013-07-01

    Variation in methods and measures, resulting in past dispute over the existence of population handedness in nonhuman great apes, has impeded progress into the origins of human right-handedness and how it relates to the human hallmark of language. Pooling evidence from behavioral studies, neuroimaging and neuroanatomy, we evaluate data on manual and cerebral laterality in humans and other apes engaged in a range of manipulative tasks and in gestural communication. A simplistic human/animal partition is no longer tenable, and we review four (nonexclusive) possible drivers for the origin of population-level right-handedness: skilled manipulative activity, as in tool use; communicative gestures; organizational complexity of action, in particular hierarchical structure; and the role of intentionality in goal-directed action. Fully testing these hypotheses will require developmental and evolutionary evidence as well as modern neuroimaging data. PMID:23546932

  8. Psychohistorical Hypotheses on Japan's History of Hostility Towards China.

    PubMed

    Wang, Bo; Rudmin, Floyd

    2016-01-01

    The accelerating tensions and military posturing between Japan and China have created a serious crisis with a danger of a catastrophic war. The purpose of this paper is to summarize the events of the current crisis, and to put it in the context of Japan's long history of hostility to China and repeated attempts at conquest. The historical record shows that Japan has attacked China at least seven times, even though China has never attacked Japan. The irrationality of Japan's behavior is demonstrated by the repetition of this hostile behavior despite the enormous human and economic costs that Japan has suffered because of it. The irrationality of Japan's militarism suggests that psychological explanations may be required to understand this phenomenon. Several hypotheses are proposed, including 1) projected paranoid aggression, 2) collective Zeigarnik compulsion, 3) perceived weakness exciting aggression, 4) national inferiority feelings, 5) cultural narcissism, and 6) Oedipal-like hatred of a parent culture. PMID:27480012

  9. Optimum testing of multiple hypotheses in quantum detection theory

    NASA Technical Reports Server (NTRS)

    Yuen, H. P.; Kennedy, R. S.; Lax, M.

    1975-01-01

    The problem of specifying the optimum quantum detector in multiple hypotheses testing is considered for application to optical communications. The quantum digital detection problem is formulated as a linear programming problem on an infinite-dimensional space. A necessary and sufficient condition is derived by the application of a general duality theorem specifying the optimum detector in terms of a set of linear operator equations and inequalities. Existence of the optimum quantum detector is also established. The optimality of commuting detection operators is discussed in some examples. The structure and performance of the optimal receiver are derived for the quantum detection of narrow-band coherent orthogonal and simplex signals. It is shown that modal photon counting is asymptotically optimum in the limit of a large signaling alphabet and that the capacity goes to infinity in the absence of a bandwidth limitation.

  10. Platinum(iv) anticancer prodrugs - hypotheses and facts.

    PubMed

    Gibson, Dan

    2016-08-16

    In this manuscript we focus on Pt(iv) anticancer prodrugs. We explore the main working hypotheses for the design of effective Pt(iv) prodrugs and note the exceptions to the common assumptions that are prevalent in the field. Special attention was devoted to the emerging class of "dual action" Pt(iv) prodrugs, where bioactive ligands are conjugated to the axial positions of platinum in order to obtain orthogonal or complementary effects that will increase the efficacy of killing the cancer cells. We discuss the rationale behind the design of the "dual action" prodrugs and the results of the pharmacological studies obtained. Simultaneous release of two bioactive moieties inside the cancer cells often triggers several processes that together determine the fate of the cell. Pt(iv) complexes provide many opportunities for applying new concepts in targeting, synergistic cell killing and exploiting novel nanodelivery systems. PMID:27214873

  11. Testing composite parametrical hypotheses without applying the reduction

    NASA Astrophysics Data System (ADS)

    Vlasov, V.; Vlasova, S.; Tolokonsky, A.

    2016-01-01

    Usually when the parametrical hypotheses are being tested the Wald reduction from composite hypothesis to the simple one is used. However, in order to apply the reduction method it is needed to know the distribution law of unknown parameter. Practically such a law cannot be determined precisely using the experimental data. First of all, it requires long supervision over the controlled stationary process to provide an inalterability of probability characteristics of the process. In practice the modifications in technological process could be made, and therefore the probability characteristics of the process can also change. Using the example of exponential distribution the algorithm of testing composite parametrical hypothesis about the distribution parameter which does not exceed the declared threshold value without use of reduction is considered in article. Such approach is based on the fact that the partition boundary of the sample space depends monotonously on unknown value of the interest parameter.

  12. Hypotheses to explain the origin of species in Amazonia.

    PubMed

    Haffer, J

    2008-11-01

    The main hypotheses proposed to explain barrier formation separating populations and causing the differentiation of species in Amazonia during the course of geological history are based on different factors, as follow: (1) Changes in the distribution of land and sea or in the landscape due to tectonic movements or sea level fluctuations (Paleogeography hypothesis), (2) the barrier effect of Amazonian rivers (River hypothesis), (3) a combination of the barrier effect of broad rivers and vegetational changes in northern and southern Amazonia (River-refuge hypothesis), (4) the isolation of humid rainforest blocks near areas of surface relief in the periphery of Amazonia separated by dry forests, savannas and other intermediate vegetation types during dry climatic periods of the Tertiary and Quaternary (Refuge hypothesis), (5) changes in canopy-density due to climatic reversals (Canopy-density hypothesis) (6) the isolation and speciation of animal populations in small montane habitat pockets around Amazonia due to climatic fluctuations without major vegetational changes (Museum hypothesis), (7) competitive species interactions and local species isolations in peripheral regions of Amazonia due to invasion and counterinvasion during cold/warm periods of the Pleistocene (Disturbance-vicariance hypothesis) and (8) parapatric speciation across steep environmental gradients without separation of the respective populations (Gradient hypothesis). Several of these hypotheses probably are relevant to a different degree for the speciation processes in different faunal groups or during different geological periods. The basic paleogeography model refers mainly to faunal differentiation during the Tertiary and in combination with the Refuge hypothesis. Milankovitch cycles leading to global main hypotheses proposed to explain barrier formation separating populations and causing the differentiation of species in Amazonia during the course of geological history are based on different

  13. Geologic setting of an unusual Martian channel - Hypotheses on origin

    NASA Technical Reports Server (NTRS)

    Scott, D. H.; Chapman, M. G.

    1989-01-01

    Several areas within the Memnonia region of Mars have been proposed as candidate sites for a Mars sample return mission. Geologic studies of these areas made from computer-enhanced high-resolution Viking images show that an assemblage of rocks having different ages and compositions are accessible to a roving vehicle. In addition, evidence of recent fluvial episodes is indicated by small channels that incises materials emplaced during the Amazonian Period. The channel discussed in this paper is located near the highland-lowland boundary in the Memnonia MC-16SW quadrangle of Mars. It is of particular interest because of distinctive morphologic characteristics compared to other Martian channels. Although several hypotheses are advanced to explain the origin of the channel, none of the arguments are completely satisfactory. However, it is believed that water mobilized from ice in the subjacent regolith (hypothesis 1) or that condensate water from highly volatile ash flows (hypothesis 2) are the most likely origins for the channel.

  14. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies. PMID:18158914

  15. Hypotheses for Near-Surface Exchange of Methane on Mars

    NASA Astrophysics Data System (ADS)

    Hu, Renyu; Bloom, A. Anthony; Gao, Peter; Miller, Charles E.; Yung, Yuk L.

    2016-07-01

    The Curiosity rover recently detected a background of 0.7 ppb and spikes of 7 ppb of methane on Mars. This in situ measurement reorients our understanding of the Martian environment and its potential for life, as the current theories do not entail any geological source or sink of methane that varies sub-annually. In particular, the 10-fold elevation during the southern winter indicates episodic sources of methane that are yet to be discovered. Here we suggest a near-surface reservoir could explain this variability. Using the temperature and humidity measurements from the rover, we find that perchlorate salts in the regolith deliquesce to form liquid solutions, and deliquescence progresses to deeper subsurface in the season of the methane spikes. We therefore formulate the following three testable hypotheses. The first scenario is that the regolith in Gale Crater adsorbs methane when dry and releases this methane to the atmosphere upon deliquescence. The adsorption energy needs to be 36 kJ/mol to explain the magnitude of the methane spikes, higher than existing laboratory measurements. The second scenario is that microorganisms convert organic matter in the soil to methane when they are in liquid solutions. This scenario does not require regolith adsorption, but entails extant life on Mars. The third scenario is that deep subsurface aquifers produce the bursts of methane. Continued in situ measurements of methane and water, as well as laboratory studies of adsorption and deliquescence, will test these hypotheses and inform the existence of the near-surface reservoir and its exchange with the atmosphere.

  16. More Specific Signal Detection in Functional Magnetic Resonance Imaging by False Discovery Rate Control for Hierarchically Structured Systems of Hypotheses

    PubMed Central

    Schildknecht, Konstantin; Tabelow, Karsten; Dickhaus, Thorsten

    2016-01-01

    Signal detection in functional magnetic resonance imaging (fMRI) inherently involves the problem of testing a large number of hypotheses. A popular strategy to address this multiplicity is the control of the false discovery rate (FDR). In this work we consider the case where prior knowledge is available to partition the set of all hypotheses into disjoint subsets or families, e. g., by a-priori knowledge on the functionality of certain regions of interest. If the proportion of true null hypotheses differs between families, this structural information can be used to increase statistical power. We propose a two-stage multiple test procedure which first excludes those families from the analysis for which there is no strong evidence for containing true alternatives. We show control of the family-wise error rate at this first stage of testing. Then, at the second stage, we proceed to test the hypotheses within each non-excluded family and obtain asymptotic control of the FDR within each family at this second stage. Our main mathematical result is that this two-stage strategy implies asymptotic control of the FDR with respect to all hypotheses. In simulations we demonstrate the increased power of this new procedure in comparison with established procedures in situations with highly unbalanced families. Finally, we apply the proposed method to simulated and to real fMRI data. PMID:26914144

  17. Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes).

    PubMed

    Melo, Bruno F; Sidlauskas, Brian L; Hoekzema, Kendra; Frable, Benjamin W; Vari, Richard P; Oliveira, Claudio

    2016-09-01

    Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semaprochilodus are resolved. The morphologically similar P. brevis, P. lacustris, P. nigricans and P. rubrotaeniatus are embedded within what is herein designated as the P. nigricans group. Species limits and distributions of these species are problematic and the group clearly merits taxonomic revision. PMID:27262428

  18. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians

    PubMed Central

    Bonetti, Maria Fernanda; Wiens, John J.

    2014-01-01

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change. PMID:25274369

  19. Phylogenetic mapping of bacterial morphology

    NASA Technical Reports Server (NTRS)

    Siefert, J. L.; Fox, G. E.

    1998-01-01

    The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

  20. Phylogenetic development of myelin glycosphingolipids.

    PubMed

    Kishimoto, Y

    1986-12-15

    Myelin is a highly specialized membrane, which enwraps axons and facilitates saltatory nerve conduction in vertebrates. Galactocerebroside and its sulfate ester, sulfatide, are highly localized in myelin. To understand the role played by these galactosphingolipids we investigated the changes of these myelin-specific compounds during the course of the evolution of myelin. We found that urodele nerve myelin lacks alpha-hydroxy fatty acid-containing galactosphingolipids. Our morphological and physiological studies of urodele nerves indicated that these hydroxy fatty acid-containing galactosphingolipids probably contribute to fast nerve conduction. Also it is suspected that they are involved in the regulation of the thickness of myelin in relation to the size of the axon. In another study, we discovered that glucocerebroside, which has glucose instead of galactose as its carbohydrate component, is abundantly present in the myelin-like sheath membrane of crustacean nerves. Subsequently, the phylogenetic study indicated that galactocerebrosides were limited to the nervous system of deuterostomes, while all protostome nerves contain glucocerebrosides. The role of glucocerebrosides in multilayered membranes and in the conduction velocity of the protostome nervous system is discussed. PMID:3549016

  1. Maximum longevities of chemically protected and non-protected fishes, reptiles, and amphibians support evolutionary hypotheses of aging.

    PubMed

    Blanco, M Andres; Sherman, Paul W

    2005-01-01

    Evolutionary hypotheses of aging predict that species with low rates of mortality from extrinsic sources, such as predation, should senesce more slowly and have longer maximum life spans than related species with higher rates of extrinsic mortality. We tested this prediction by synthesizing information on maximum body lengths and life spans in captivity of 1193 species of chemically protected (venomous or poisonous) and non-chemically protected fishes, snakes, caudatans (salamanders and newts), and anurans (frogs and toads). In every phylogenetic group maximum longevity was positively correlated with body size and, when size was controlled for statistically, chemically protected species and genera usually had longer maximum life spans than non-protected species. These results reemphasize the importance of life history traits, particularly protection from predation, in the evolution of senescence. PMID:15888334

  2. Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

    PubMed Central

    van Hazel, Ilke; Santini, Francesco; Müller, Johannes; Chang, Belinda SW

    2006-01-01

    Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction. PMID:17107620

  3. Evolution of specialization: a phylogenetic study of host range in the red milkweed beetle (Tetraopes tetraophthalmus).

    PubMed

    Rasmann, Sergio; Agrawal, Anurag A

    2011-06-01

    Specialization is common in most lineages of insect herbivores, one of the most diverse groups of organisms on earth. To address how and why specialization is maintained over evolutionary time, we hypothesized that plant defense and other ecological attributes of potential host plants would predict the performance of a specialist root-feeding herbivore (the red milkweed beetle, Tetraopes tetraophthalmus). Using a comparative phylogenetic and functional trait approach, we assessed the determinants of insect host range across 18 species of Asclepias. Larval survivorship decreased with increasing phylogenetic distance from the true host, Asclepias syriaca, suggesting that adaptation to plant traits drives specialization. Among several root traits measured, only cardenolides (toxic defense chemicals) correlated with larval survival, and cardenolides also explained the phylogenetic distance effect in phylogenetically controlled multiple regression analyses. Additionally, milkweed species having a known association with other Tetraopes beetles were better hosts than species lacking Tetraopes herbivores, and milkweeds with specific leaf area values (a trait related to leaf function and habitat affiliation) similar to those of A. syriaca were better hosts than species having divergent values. We thus conclude that phylogenetic distance is an integrated measure of phenotypic and ecological attributes of Asclepias species, especially defensive cardenolides, which can be used to explain specialization and constraints on host shifts over evolutionary time. PMID:21597250

  4. Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group).

    PubMed

    Geneva, Anthony J; Hilton, Jared; Noll, Sabina; Glor, Richard E

    2015-06-01

    The distichus species group includes six species and 21 subspecies of trunk ecomorph anoles distributed across Hispaniola and its satellite islands as well as the northern Bahamas. Although this group has long served as a model system for studies of reproductive character displacement, adaptation, behavior and speciation, it has never been the subject of a comprehensive phylogenetic analysis. Our goal here is to generate a multilocus phylogenetic dataset (one mitochondrial and seven nuclear loci) and to use this dataset to infer phylogenetic relationships among the majority of the taxa assigned to the distichus species group. We use these phylogenetic trees to address three topics about the group's evolution. First, we consider longstanding taxonomic controversies about the status of several species and subspecies assigned to the distichus species group. Second, we investigate the biogeographic history of the group and specifically test the hypotheses that historical division of Hispaniola into two paleo-islands contributed to the group's diversification and that Bahamian and Hispaniolan satellite island populations are derived from colonists from the main Hispaniolan landmass. Finally, third, we use comparative phylogenetic analyses to test the hypothesis that divergence between pale yellow and darkly pigmented orange or red dewlap coloration has occurred repeatedly across the distichus species group. PMID:25772800

  5. Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)

    USGS Publications Warehouse

    Moyle, R.G.; Chesser, R.T.; Brumfield, R.T.; Tello, J.G.; Marchese, D.J.; Cracraft, J.

    2009-01-01

    The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. ?? 2009 The Willi Hennig Society.

  6. Phylogenetic trait conservation in the partner choice of a group of ectomycorrhizal trees.

    PubMed

    Hayward, Jeremy; Horton, Thomas R

    2014-10-01

    Ecological interactions are frequently conserved across evolutionary time. In the case of mutualisms, these conserved interactions may play a large role in structuring mutualist communities. We hypothesized that phylogenetic trait conservation could play a key role in determining patterns of association in the ectomycorrhizal symbiosis, a globally important trophic mutualism. We used the association between members of the pantropical plant tribe Pisonieae and its fungal mutualist partners as a model system to test the prediction that Pisonieae-associating ectomycorrhizal fungi will be more closely related than expected by chance, reflecting a conserved trait. We tested this prediction using previously published and newly generated sequences in a Bayesian framework incorporating phylogenetic uncertainty. We report that phylogenetic trait conservation does exist in this association. We generated a five-marker phylogeny of members of the Pisonieae and used this phylogeny in a Bayesian relaxed molecular clock analysis. We established that the most recent common ancestors of Pisonieae species and Pisonieae-associating fungi sharing phylogenetic conservation of their patterns of ectomycorrhizal association occurred no more recently than 14.2 Ma. We therefore suggest that phylogenetic trait conservation in the Pisonieae ectomycorrhizal mutualism association represents an inherited syndrome which has existed for at least 14 Myr. PMID:25169622

  7. Incorporating clade identity in analyses of phylogenetic community structure: an example with hummingbirds.

    PubMed

    Parra, Juan L; McGuire, Jimmy A; Graham, Catherine H

    2010-11-01

    An important challenge in community ecology is to determine how processes occurring at multiple spatial, temporal, and phylogenetic scales influence the structure of local communities. While indexes of phylogenetic structure, which measure how related species are in a community, provide insight into the processes that shape species coexistence, they fail to pinpoint the phylogenetic scales at which those processes occur. Here, we explore a framework to identify the species and clades responsible for the inferred patterns of phylogenetic structure within a given community. Further, we evaluate how communities that share the nonrandom representation of species from a given clade in the phylogeny are distributed across geography and environmental gradients. Using Ecuadorian hummingbird communities, we found that multiple patterns of phylogenetic structure often occur within a local assemblage. We also identified four geographic regions where species from certain clades exhibit nonrandom representation: the eastern Amazonian lowlands, the western dry lowlands, the Andes at middle elevations, and the Andes at high elevations. The environmental gradients along which changes in the local coexistence of species occurred were mainly elevation, annual precipitation, and seasonality in both temperature and precipitation. Finally, we show how these patterns can be used to generate hypotheses about the processes that allow species coexistence. PMID:20849270

  8. Spatial overlap in a solitary carnivore: support for the land tenure, kinship or resource dispersion hypotheses?

    PubMed

    Elbroch, L Mark; Lendrum, Patrick E; Quigley, Howard; Caragiulo, Anthony

    2016-03-01

    There are several alternative hypotheses about the effects of territoriality, kinship and prey availability on individual carnivore distributions within populations. The first is the land-tenure hypothesis, which predicts that carnivores regulate their density through territoriality and temporal avoidance. The second is the kinship hypothesis, which predicts related individuals will be clumped within populations, and the third is the resource dispersion hypothesis, which suggests that resource richness may explain variable sociality, spatial overlap or temporary aggregations of conspecifics. Research on the socio-spatial organization of animals is essential in understanding territoriality, intra- and interspecific competition, and contact rates that influence diverse ecology, including disease transmission between conspecifics and courtship behaviours. We explored these hypotheses with data collected on a solitary carnivore, the cougar (Puma concolor), from 2005 to 2012 in the Southern Yellowstone Ecosystem, Wyoming, USA. We employed 27 annual home ranges for 13 cougars to test whether home range overlap was better explained by land tenure, kinship, resource dispersion or some combination of the three. We found support for both the land tenure and resource dispersion hypotheses, but not for kinship. Cougar sex was the primary driver explaining variation in home range overlap. Males overlapped significantly with females, whereas the remaining dyads (F-F, M-M) overlapped significantly less. In support for the resource dispersion hypothesis, hunting opportunity (the probability of a cougar killing prey in a given location) was often higher in overlapping than in non-overlapping portions of cougar home ranges. In particular, winter hunt opportunity rather than summer hunt opportunity was higher in overlapping portions of female-female and male-female home ranges. Our results may indicate that solitary carnivores are more tolerant of sharing key resources with unrelated

  9. The space of ultrametric phylogenetic trees.

    PubMed

    Gavryushkin, Alex; Drummond, Alexei J

    2016-08-21

    The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. PMID:27188249

  10. Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

    PubMed Central

    Lang, Daniel; Weiche, Benjamin; Timmerhaus, Gerrit; Richardt, Sandra; Riaño-Pachón, Diego M.; Corrêa, Luiz G. G.; Reski, Ralf; Mueller-Roeber, Bernd; Rensing, Stefan A.

    2010-01-01

    Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity. PMID:20644220

  11. Eastern Scotian Shelf trophic dynamics: A review of the evidence for diverse hypotheses

    NASA Astrophysics Data System (ADS)

    Sinclair, Michael; Power, Michael; Head, Erica; Li, William K. W.; McMahon, Michael; Mohn, Robert; O'Boyle, Robert; Swain, Douglas; Tremblay, John

    2015-11-01

    Two hypotheses have been proposed to account for trophic dynamic control of the eastern Scotian Shelf ecosystem off Atlantic Canada: (1) top-down: fishery induced trophic cascade and (2) bottom-up: climate variability. We evaluate the evidence in support of these hypotheses: including observations on top-down drivers (fishing effort and predation by grey seals), bottom-up drivers (nutrient supply and water column stratification), and the several trophic levels (groundfish, macro-invertebrates, small pelagic fish, and plankton). There is limited support for the fishery-induced trophic cascade hypothesis. The predictions of the climate variability hypothesis are generally met for the lower and middle trophic levels, but the ongoing high levels of natural mortality of groundfish are not accounted for. We propose an alternative hypothesis encompassing concurrent top-down and bottom-up processes, and conclude that many species of groundfish (including cod) and small pelagic fish stocks (including herring) will not recover with the ongoing high levels of natural mortality generated by grey seal predation. Predictions on future trends in abundance of the commercially important macro-invertebrate species (lobster, snow crab, and shrimp) are not possible based on the available evidence.

  12. Testing hypotheses of bird extinctions at Rio Palenque, Ecuador, with informal species lists.

    PubMed

    Pearson, David L; Anderson, Corey Devin; Mitchell, Brian R; Rosenberg, Michael S; Navarrete, Ronald; Coopmans, Paul

    2010-04-01

    Informally gathered species lists are a potential source of data for conservation biology, but most remain unused because of questions of reliability and statistical issues. We applied two alternative analytical methods (contingency tests and occupancy modeling) to a 35-year data set (1973-2007) to test hypotheses about local bird extinction. We compiled data from bird lists collected by expert amateurs and professional scientists in a 2-km(2) fragment of lowland tropical forest in coastal Ecuador. We tested the effects of the following on local extinction: trophic level, sociality, foraging specialization, light tolerance, geographical range area, and biogeographic source. First we assessed extinction on the basis of the number of years in which a species was not detected on the site and used contingency tests with each factor to compare the frequency of expected and observed extinction events among different species categories. Then we defined four multiyear periods that reflected different stages of deforestation and isolation of the study site and used occupancy modeling to test extinction hypotheses singly and in combination. Both types of analyses supported the biogeographic source hypothesis and the species-range hypothesis as causes of extinction; however, occupancy modeling indicated the model incorporating all factors except foraging specialization best fit the data. PMID:20028414

  13. MM-Correction: Meta-analysis-Based Multiple Hypotheses Correction in Omic Studies

    NASA Astrophysics Data System (ADS)

    Nardini, Christine; Wang, Lei; Peng, Hesen; Benini, Luca; Kuo, Michael D.

    The post-Genomic Era is characterized by the proliferation of high-throughput platforms that allow the parallel study of a complete body of molecules in one single run of experiments (omic approach). Analysis and integration of omic data represent one of the most challenging frontiers for all the disciplines related to Systems Biology. From the computational perspective this requires, among others, the massive use of automated approaches in several steps of the complex analysis pipeline, often consisting of cascades of statistical tests. In this frame, the identification of statistical significance has been one of the early challenges in the handling of omic data and remains a critical step due to the multiple hypotheses testing issue, given the large number of hypotheses examined at one time. Two main approaches are currently used: p-values based on random permutation approaches and the False Discovery Rate. Both give meaningful and important results, however they suffer respectively from being computationally heavy -due to the large number of data that has to be generated-, or extremely flexible with respect to the definition of the significance threshold, leading to difficulties in standardization. We present here a complementary/alternative approach to these current ones and discuss performances, properties and limitations.

  14. Phylogenetic patterns of climatic, habitat and trophic niches in a European avian assemblage

    PubMed Central

    Pearman, Peter B; Lavergne, Sébastien; Roquet, Cristina; Wüest, Rafael; Zimmermann, Niklaus E; Thuiller, Wilfried

    2014-01-01

    Aim The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. Location Europe. Methods From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence. Results In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. Main conclusions Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on

  15. ftz evolution: findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019).

    PubMed

    Heffer, Alison; Löhr, Ulrike; Pick, Leslie

    2011-12-01

    In a recent paper, Merabet and Hudry discuss models explaining the functional evolution of fushi tarazu (ftz) from an ancestral homeotic to a pair-rule segmentation gene in Drosophila. As most of the experimental work underlying these models comes from our research, we wish to reply to Merabet and Hudry providing an explanation of the experimental approaches and logical framework underlying them. We review experimental data that support our hypotheses and discuss misconceptions in the literature. We emphasize that the change in ftz function required changes in both expression pattern and protein function and review the evidence that these functional changes involved a switch in cofactor-interaction motifs during arthropod radiations. While agreeing with Merabet and Hudry that protein context likely contributes to Ftz function, we argue that until supporting evidence for alternative mechanisms is obtained, the role of cofactor-interaction motifs in driving a functional switch remains compelling. PMID:22113740

  16. Landscape moderation of biodiversity patterns and processes - eight hypotheses.

    PubMed

    Tscharntke, Teja; Tylianakis, Jason M; Rand, Tatyana A; Didham, Raphael K; Fahrig, Lenore; Batáry, Péter; Bengtsson, Janne; Clough, Yann; Crist, Thomas O; Dormann, Carsten F; Ewers, Robert M; Fründ, Jochen; Holt, Robert D; Holzschuh, Andrea; Klein, Alexandra M; Kleijn, David; Kremen, Claire; Landis, Doug A; Laurance, William; Lindenmayer, David; Scherber, Christoph; Sodhi, Navjot; Steffan-Dewenter, Ingolf; Thies, Carsten; van der Putten, Wim H; Westphal, Catrin

    2012-08-01

    Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on

  17. An automated framework for hypotheses generation using literature

    PubMed Central

    2012-01-01

    Background In bio-medicine, exploratory studies and hypothesis generation often begin with researching existing literature to identify a set of factors and their association with diseases, phenotypes, or biological processes. Many scientists are overwhelmed by the sheer volume of literature on a disease when they plan to generate a new hypothesis or study a biological phenomenon. The situation is even worse for junior investigators who often find it difficult to formulate new hypotheses or, more importantly, corroborate if their hypothesis is consistent with existing literature. It is a daunting task to be abreast with so much being published and also remember all combinations of direct and indirect associations. Fortunately there is a growing trend of using literature mining and knowledge discovery tools in biomedical research. However, there is still a large gap between the huge amount of effort and resources invested in disease research and the little effort in harvesting the published knowledge. The proposed hypothesis generation framework (HGF) finds “crisp semantic associations” among entities of interest - that is a step towards bridging such gaps. Methodology The proposed HGF shares similar end goals like the SWAN but are more holistic in nature and was designed and implemented using scalable and efficient computational models of disease-disease interaction. The integration of mapping ontologies with latent semantic analysis is critical in capturing domain specific direct and indirect “crisp” associations, and making assertions about entities (such as disease X is associated with a set of factors Z). Results Pilot studies were performed using two diseases. A comparative analysis of the computed “associations” and “assertions” with curated expert knowledge was performed to validate the results. It was observed that the HGF is able to capture “crisp” direct and indirect associations, and provide knowledge discovery on demand. Conclusions

  18. On Tree-Based Phylogenetic Networks.

    PubMed

    Zhang, Louxin

    2016-07-01

    A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model. PMID:27228397

  19. Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

    NASA Astrophysics Data System (ADS)

    Xia, Xuhua

    Phylogenetic relationship is essential in dating evolutionary events, reconstructing ancestral genes, predicting sites that are important to natural selection, and, ultimately, understanding genomic evolution. Three categories of phylogenetic methods are currently used: the distance-based, the maximum parsimony, and the maximum likelihood method. Here, I present the mathematical framework of these methods and their rationales, provide computational details for each of them, illustrate analytically and numerically the potential biases inherent in these methods, and outline computational challenges and unresolved problems. This is followed by a brief discussion of the Bayesian approach that has been recently used in molecular phylogenetics.

  20. Exploration of miRNA families for hypotheses generation

    NASA Astrophysics Data System (ADS)

    Kamanu, Timothy K. K.; Radovanovic, Aleksandar; Archer, John A. C.; Bajic, Vladimir B.

    2013-10-01

    Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

  1. Plant reproduction systems in microgravity: experimental data and hypotheses

    NASA Astrophysics Data System (ADS)

    Kordyum, E. L.

    Elucidation of the possibilities for higher plants to realize complete ontogenesis, from seed to seed, and to propagate by seeds in microgravity, is a fundamental task of space biology connected with the working of the CELSS program. At present, there are results of only 6 spaceflight experiments with Arabidopsis thaliana, an ephemeral plant which will flower and fruit in orbit. Morphogenesis of generative organs occurs normally in microgravity, but unlike the ground control, buds and flowers mainly contain sterile elements of the androecium and gynoecium which degenerate at different stages of development in microgravity. Cytological peculiarities of male and female sterility in microgravity are similar to those occurring naturally during sexual differentiation. Many of the seed formed in microgravity are: 1) nutritional deficiency, 2) insufficient light, 3) intensification of the influence of the above-mentioned factors by microgravity, 4) disturbances of a hormonal nature, and 5) the absence of pollination and fertilization. Possible ways for testing these hypotheses and obtaining viable seeds in microgravity are discussed.

  2. [The thought-brain relationship. New facts. New hypotheses].

    PubMed

    Laplane, D

    1985-01-01

    The close links between Thought and the brain having been amply demonstrated by the neurosciences, it is now time to draw conclusions. After having shown that the specific characteristic of thought is the self, the author underlines the impossibility of explaining the self by objective study and the consequent need to preserve for the thought its specificity in relation to Matter-Energy. After having excluded, by this statement, attitudes tending to deny explicitly or implicitly the specificity of Thought and having rejected spiritualist hypotheses as not conforming to scientific data, only two possible interpretations remain: that of the identity of Thought and Matter-Energy treats Thought as the other face of Energy, that of creation makes it necessary to admit a transformation from Energy to Thought (E = KP). The problems of thermodynamics and of the quantification of Thought thus raised are considered. Whatever the solution, it is necessary to admit that a "Universal Thought" exists. The universe is conscious of itself. The effort of cerebralisation in the evolution of species seems a mean of giving autonomy to individual thought which is necessarily included in Universal Thought. PMID:3996289

  3. [Age-prospective memory-paradox: explanatory hypotheses].

    PubMed

    Azzopardi, Barbara; Auffray, Caroline; Juhel, Jacques

    2015-03-01

    Prospective memory is a complex cognitive function requiring to remember a planned action. For example, this function is particularly important for elderly people to remember taking medication at the appropriate time. The comparison of the performance of old and young peoples on different prospective memory tasks led to two contradictory results, a configuration that has been dubbed "age-prospective memory-paradox". The first set of results of the age-prospective memory-paradox configuration is in keeping with the effects of aging on cognitive functioning, older peoples generally performing less well than younger peoples on laboratory prospective memory tasks. The second set of results is at odds with the first one, as older peoples generally perform better than younger peoples on naturalistic prospective memory tasks. The aim of the present paper is to expose the main explanatory hypotheses of the age related deficit on laboratory prospective memory tasks in one hand and on the age related benefit on naturalistic prospective memory tasks on the other hand. Concerning laboratory prospective memory tasks, the main hypothesis is that the detrimental effect of age would be principally due to negative influence of age on executive control processes and retrospective memory processes involved in this kind of tasks. With respect to naturalistic prospective memory tasks, a higher motivational level and the fact that older people have more frequently recourse to external memory aids and to compensation strategies could explain the better results of older people. PMID:25786425

  4. Exploration of miRNA families for hypotheses generation.

    PubMed

    Kamanu, Timothy K K; Radovanovic, Aleksandar; Archer, John A C; Bajic, Vladimir B

    2013-01-01

    Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific. PMID:24126940

  5. Intestinal protozoa are hypothesized to stimulate immunosurveillance against colon cancer.

    PubMed

    Juckett, David A; Aylsworth, Charles F; Quensen, Janet Murphy

    2008-01-01

    Colon cancer in humans results in considerable morbidity and mortality throughout most of the world. During the twentieth century, there was a rapid rise in colon cancer within modernizing countries that has not been adequately explained, although the role of diet has been widely explored. Previously, we showed that the presence of the endemic Eimeria spp. protozoan in intestinal tissues is associated with regions of low tumorigenesis in the large and small bovine intestine and that an Eimeria surface protein is a potent activator of dendritic cells and a useful immunomodulator, with anti-cancer and anti-viral properties. Therefore, we hypothesize that the persistent presence of such an intestinal protozoan enhances immunosurveillance by elevating the intestinal alert status and that the loss of these organisms could lead to a higher incidence of colon cancer. Preliminary support of this hypothesis derives from the observations that domestic animals, known to maintain this protozoan, have very low colon cancer incidence. We propose that this also may occur in human populations that use human excrement (night soil) as a fertilizer, a practice that serves to complete the life cycle of this type of microbe. We examine some evidence for this hypothesis in Japan's mortality patterns, where we show that colon cancer increased after the cessation of night soil use, but before the change to a western diet. We conclude that this hypothesis, a variation of the hygiene hypothesis, is worth further consideration and continued elaboration. PMID:18343044

  6. Phylogenetic relationships among subsurface microorganisms

    SciTech Connect

    Nierzwicki-Bauer, S.A.

    1991-01-01

    This report summarizes the progress made from 6/90--3/91 toward completion of our project, Phylogenetic Relationships among subsurface microorganisms. 16S rRNA was sequenced, and based on the sequence the SMCC isolates were assigned to preliminary groups. Microorganisms were obtained at various depths at the Savannah River Site, including the Surface (0 m), Congaree (91 m), and Middendorf (244 m, 259 m, 265 m). Sequence data from four isolates from the Congaree formation indicate these microorganisms can be divided into Pseudomonas spp. or Acinetobacter spp. Three 16S rRNA probes were synthesized based on sequence data. The synthesized probes were tested through in situ hybridization. Optimal conditions for in situ hybridization were determined. Because stability of RNA-DNA hybrids is dependent on hybridization stringency, related organisms can be differentiated using a single probe under different strigencies. The results of these hybridizations agree with results obtained by Balkwill and Reeves using restriction fragment length polymorphism analysis. The RNA content of a cell reflects its metabolic state. Cells which are starved for four days are not detectable with the homologous 16S rRNA probe. However, within 15 minutes of refeeding, detectable rRNA appeared. This suggests that organisms which are undetectable in environmental samples due to starvation may be detectable after addition of nutrients. Stepwise addition of specific nutrients could indicate which nutrients are rate limiting for growth. Preliminary experiments with soil samples from the Hanford Site indicate indigenous microorganisms can be detected by oligionucleotide probes. Further, using multiple probes based on universal sequences increases the number of organisms detected. Double label experiments, using a rhodamine-labelled oligionucleotide probe with free coumarin succinimidyl ester will allow simultaneous detection of total bacteria and specific 16S rRNA containing bacteria. 4 tabs. (MHB)

  7. Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses

    PubMed Central

    Smith, M. Alex; Eveleigh, Eldon S.; McCann, Kevin S.; Merilo, Mark T.; McCarthy, Peter C.; Van Rooyen, Kathleen I.

    2011-01-01

    The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana – SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD) – the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the “bird feeder effect”) and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future

  8. The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

    PubMed Central

    Larsson, Hans C.E.; Habib, Michael B.

    2016-01-01

    Background: Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping. Methods: Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground truthed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds. Results: None of these behaviours were found to meet the biomechanical threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa like Microraptor and Archaeopteryx. Discussion: Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this

  9. Phylogenetics and the origin of species

    PubMed Central

    Avise, John C.; Wollenberg, Kurt

    1997-01-01

    A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive ties are related aspects of phylogeny and jointly illuminate biotic discontinuity. PMID:9223259

  10. TIPP: taxonomic identification and phylogenetic profiling

    PubMed Central

    Nguyen, Nam-phuong; Mirarab, Siavash; Liu, Bo; Pop, Mihai; Warnow, Tandy

    2014-01-01

    Motivation: Abundance profiling (also called ‘phylogenetic profiling’) is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn. Availability and implementation: Software and supplementary materials are available at http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25359891